Structure Of Complex Research Articles

Two-stage binding of mitochondrial ferredoxin-2 to the core iron-sulfur cluster assembly complex

Iron-sulfur (FeS) protein biogenesis in eukaryotes begins with the de novo assembly of [2Fe-2S] clusters by the mitochondrial core iron-sulfur cluster assembly (ISC) complex. This complex comprises the scaffold protein ISCU2, the cysteine desulfurase subcomplex NFS1-ISD11-ACP1, the allosteric activator frataxin (FXN) and the electron donor ferredoxin-2 (FDX2). The structural interaction of FDX2 with the complex remains unclear. Here, we present cryo-EM structures of the human FDX2-bound core ISC complex showing that FDX2 and FXN compete for overlapping binding sites. FDX2 binds in either a ‘distal’ conformation, where its helix F interacts electrostatically with an arginine patch of NFS1, or a ‘proximal’ conformation, where this interaction tightens and the FDX2-specific C terminus binds to NFS1, facilitating the movement of the [2Fe-2S] cluster of FDX2 closer to the ISCU2 FeS cluster assembly site for rapid electron transfer. Structure-based mutational studies verify the contact areas of FDX2 within the core ISC complex.

Enantiomorphic single component conducting nickel(II) and platinum(II) bis(diethyl-dddt) crystalline complexes.

Monoanionic and neutral nickel(II) and platinum(II) bis(dithiolene) complexes based on the 5,6-diethyl-5,6-dihydro-1,4-dithiin-2,3-dithiolate (de-dddt) chiral ligand have been prepared in racemic and enantiopure forms. Neutral closed-shell species have been generated from monoanionic precursors upon electrocrystallization. The racemic anionic (TBA)[Ni(S,S-de-dddt)(R,R-de-dddt)] complex crystallized in the centrosymmetric space group P21/c, while the neutral complexes crystallized in the enantiomorphic tetragonal space group P41212 or P43212. Very subtle conformational differences concerning the orientation of the ethyl substituents are observed between the racemic and the enantiopure compounds, thus impacting the intermolecular interactions at the nanoscale level. Indeed, in the former, the ethyl substituents are all-axial in both independent complexes, while in the latter, one of the independent complexes shows a mixed (eq, eq, ax, ax) conformation and the other independent complex of the asymmetric unit shows the all-axial conformation. Such a tenuous difference at the molecular/nanoscale level strongly impacts the conductivity of the materials. Temperature dependent high pressure single crystal conductivity measurements show activated conductivity for all the materials, with room temperature conductivity values of up to 1.3 × 10-3 S cm-1 for [Ni(S,S-de-dddt)2] at 12.3 GPa and 3.0 × 10-4 S cm-1 for [Pt(R,R-de-dddt)2] at 12.9 GPa. Nevertheless, the racemic compounds are more conductive, i.e. 3.8 × 10-2 S cm-1 for [Ni(rac-de-dddt)2] at 10.0 GPa and 1.5 × 10-3 S cm-1 for [Pt(rac-de-dddt)2] at 10.5 GPa, in agreement with the shorter and more numerous S⋯S intermolecular contacts observed in the crystal structures of the racemic complexes. Moreover, a detailed analysis of DFT calculations suggests that smaller band gaps and higher conductivities should occur for the racemic solids and for the Pt versus Ni complexes.

PPB-Affinity: Protein-Protein Binding Affinity dataset for AI-based protein drug discovery

Prediction of protein-protein binding (PPB) affinity plays an important role in large-molecular drug discovery. Deep learning (DL) has been adopted to predict the changes of PPB binding affinities upon mutations, but there was a scarcity of studies predicting the PPB affinity itself. The major reason is the paucity of open-source dataset with PPB affinity data. To address this gap, the current study introduced a large comprehensive PPB affinity (PPB-Affinity) dataset. The PPB-Affinity dataset contains key information such as crystal structures of protein-protein complexes (with or without protein mutation patterns), PPB affinity, receptor protein chain, ligand protein chain, etc. To the best of our knowledge, this is the largest publicly available PPB affinity dataset, and we believe it will significantly advance drug discovery by streamlining the screening of potential large-molecule drugs. We also developed a deep-learning benchmark model with this dataset to predict the PPB affinity, providing a foundational comparison for the research community.

Structural insights into the high basal activity and inverse agonism of the orphan receptor GPR6 implicated in Parkinson's disease.

GPR6 is an orphan G protein-coupled receptor with high constitutive activity found in D2-type dopamine receptor-expressing medium spiny neurons of the striatopallidal pathway, which is aberrantly hyperactivated in Parkinson's disease. Here, we solved crystal structures of GPR6 without the addition of a ligand (a pseudo-apo state) and in complex with two inverse agonists, including CVN424, which improved motor symptoms in patients with Parkinson's disease in clinical trials. In addition, we obtained a cryo-electron microscopy structure of the signaling complex between GPR6 and its cognate Gs heterotrimer. The pseudo-apo structure revealed a strong density in the orthosteric pocket of GPR6 corresponding to a lipid-like endogenous ligand. A combination of site-directed mutagenesis, native mass spectrometry, and computer modeling suggested potential mechanisms for high constitutive activity and inverse agonism in GPR6 and identified a series of lipids and ions bound to the receptor. The structures and results obtained in this study could guide the rational design of drugs that modulate GPR6 signaling.

Chiral Pd2L4 Capsules from Readily Accessible Tröger's Base Ligands Inducing Circular Dichroism on Fullerenes C60 and C70.

The induction of chirality on pristine fullerenes through non-covalent embedding in an asymmetric nano-confinement has only been rarely reported. Bringing molecules with such a unique electronic structure and broad application range into a chiral environment is particularly appealing for the development of chiroptical materials, enantioselective photoredox catalysts and systems showing chirality-induced spin selectivity (CISS). In this study, we report the formation of a chiral, configurationally stable Pd2L4capsule assembled from aC2-symmetric, 'ribbon-shaped' ligand with a Tröger's base naphthalimide (TbNaps) backbone, easily synthesized in three steps from commercially available compounds. Embedding chirality directly into the ligand backbone ensures a relatively lightweight receptor design whose aromatic panels create a strongly shielded inner cavity of about 700 Å3volume. Fullerenes C60and C70, as well as a pair of corannulenes, can be bound in acetonitrile (where unsubstituted fullerenes are insoluble) and X-ray structures of host-guest complexes were obtained. Tight interactions between the chiral host and the fullerene guests leads to the induction of a circular dichroism (CD) on the characteristic absorption bands of the forbidden π-π* transitions of the fullerenes, backed up by sTDA TD-DFT calculations and detailed investigation of the electronic excited states.

Probing host guest inclusion complex and its applications by biophysical approach subsequently optimized by molecular docking

Herein, we explored the construction of a supramolecular encapsulated complex between Nile blue (NB) and p-sulfonatothiacalix[4]arene (TSC4X). The developed inclusion complex (NB-TSC4X) was established by fluorescence spectroscopy, TGA, FTIR, 1H NMR, and DFT studies. Benesi-Hildebrand calculation showed a linear plot that indicated a 1:1 stoichiometric ratio having a fairly high stability constant of 2720 M−1 in the solution phase. DFT analysis helps us to find out the optimized structure of the inclusion complex. Finally, the binding interaction of the inclusion complex with bovine serum albumin (BSA) was evaluated. In brief, this work uncloses a new strategy to enhance the performance of fluorescent dye.

A novel layered structure of the heterometallic oxalate compound [NH2(CH3)2]2[NaFe(C2O4)3]·0.33NH(CH3)2·0.33H2O: synthesis, crystal structure and thermal decomposition.

The synthesis, single-crystal X-ray structure determination and thermal analysis are reported for a novel heteronuclear oxalate compound synthesized from a mixture of Fe and Na salts, oxalic acid and N,N-dimethylformamide (DMF) in aqueous solution. The new metallooxalate compound was obtained and identified as a dimethylammonium tris(oxalato)ferrate(III), namely, poly[[bis(dimethylammonium) [tri-μ-oxalato-sodium(I)iron(III)]]-dimethylamine-water (3/1/1)], [NH2(CH3)2]2[NaFe(C2O4)3]·0.33NH(CH3)2·0.33H2O, which crystallizes in the orthorhombic noncentrosymmetric space group C2221. In this novel structure, each Fe atom is hexacoordinated by three non-equivalent bidentate oxalate ligands, while the four Na atoms adopt different coordination numbers, i.e. 6, 7 and 8. The structure consists of bimetallic anionic A layers, {[NaFe(C2O4)3]2-}n, displaying a layered structure with infinitely linked Fe2Na2 tetramers on the ab plane. Two kinds of bimetallic parallel layers (A1 and A2) are present alternately and are found to be staggered, while only the A2 layer is crossed by a twofold axis parallel to the a axis through two Na atoms. The [NH2(CH3)2]+ (HDMA) cations occupy the voids between the anionic layers, while the free molecules, i.e. NH(CH3)2 (DMA) and H2O, are located between two different anionic layers. In addition to ionic bonds, the stability of the structure is ensured by hydrogen-bond interactions involving the oxalate ligands and the nitrogenous and water molecules. The layered structure appears to be different in the family of oxalate-bridged NaI-FeIII compounds. It is in agreement with the predicted 2D or layered structure of bimetallic complexes containing anionic tris(oxalato)metallate(III) with the [XR4]+ counter-ion template (X= N, P or S, and R= alkyl group or H). The thermal decomposition of the compound shows the final residual product to be NaFeO2.

Enzymatic, structural, and biophysical characterization of a single-domain antibody (VHH) selectively and tightly inhibiting neutrophil elastase and exhibiting favorable developability properties.

Human neutrophil elastase (hNE), a serine protease released by neutrophils during inflammation, plays a major role in the pathophysiology of several conditions especially in inflammatory lung diseases. Its inhibition constitutes, therefore, a promising therapeutic strategy to combat these diseases. In this work, we characterized the in vitro properties of a VHH (i.e., the antigen binding domain of camelid heavy chain-only antibodies), referred to as NbE201. This VHH is able to inhibit tightly, selectively and competitively both human and murine elastases with the inhibition constants (Ki) of 4.1 ± 0.9 nM and 36.8 ± 3.9 nM, respectively. The IC50 for the inhibition of the hydrolysis of elastin is in the same range to that of alpha-1 antitrypsin (i.e., the main endogenous inhibitor of hNE also used in the clinic) and 14 times better than that of Sivelestat (i.e., the 2nd clinically approved hNE inhibitor). The X-ray crystal structure of the NbE201-hNE complex reveals that the Complementarity Determining Regions CDR1 and CDR3 of the VHH bind into the substrate binding pocket of hNE and prevent the access to small or macromolecular substrates. They do not, however, bind deep enough into the pocket to be hydrolyzed. NbE201 is highly stable towards oxidation, deamidation, and chemical or thermal denaturation. NbE201 is therefore likely to tolerate manufacturing processes during drug development. These results highlight the high potential of NbE201 as a (pre)clinical tool to diagnose and treat diseases associated with excessive hNE activity, and for fundamental research to better understand the role of hNE in these conditions.

Organogermanium(IV) complexes with O,N,O’-tridentate Schiff bases: synthesis, electrochemical transformations, photophysical properties, and anti/prooxidant activity

A series of novel diorganogermanium(IV) complexes of the type [R2Ge(Ln)] (where R is Et, Ph) with O,N,O’-tridentate redox-active Schiff bases has been synthesized. Compounds 1–7 were characterized by 1H, 13C{1H} NMR, IR spectroscopy, and elemental analysis. The molecular structures of complexes 1, 3, and 7 in crystal state have been established using single-crystal X-ray analysis. The complexes are pentacoordinate mononuclear compounds of germanium(IV). The bond lengths in tridentate ligands correspond to their diamagnetic dianionic forms. The electrochemical properties of complexes 1–7 were studied by cyclic voltammetry. A feature of the electrochemical behavior of target complexes is the ability to form relatively stable reduced/oxidized species as a result of the one-electron transfer. The stability of electrogenerated forms is influenced by both the organic groups at the germanium(IV) atom and the substituents in the Schiff bases. The energy gap (ΔEel) between the boundary redox orbitals obtained from electrochemical data for the complexes varies from 2.43 to 2.60 eV, while the optical ΔE was observed in the narrow range (2.46 – 2.50 eV). Luminescent activity was detected for some complexes in the solution. The maximal values ​​of the relative quantum yield were determined for complexes containing an electron-withdrawing nitro group in the redox-active ligand. In the reaction with ABTS radical cation, compound 1 only possessed the radical scavenging activity while the other compounds are characterized by weak neutralizing properties. The dual anti/prooxidant action was observed for compounds 1–7 in the process of rat liver (Wistar) homogenate lipid peroxidation.

Structural basis for full-length chemerin recognition and signaling through chemerin receptor 1

Chemerin, a chemotactic adipokine, plays essential roles in adipogenesis and inflammation. Serum chemerin concentration is closely associated with obesity and metabolism disorders. The mature form of chemerin (residues 21-157) acts primarily through chemerin receptor 1 (CMKLR1) for transmembrane signaling. As a result, CMKLR1 serves as a promising target for therapeutic intervention of immunometabolic diseases such as diabetes and multiple sclerosis. Here, we present a high-resolution cryo-EM structure of CMKLR1-Gi signaling complex bound to biologically active full-length chemerin. The mature chemerin shows binding features distinct from its C-terminal nonapeptide including interaction with both the extracellular loops (ECLs) and the N-terminus of CMKLR1. Combining results from functional assays, our studies demonstrate that chemerin interacts with CMKLR1 in a “two-site” mode similar to chemokine-chemokine receptor interactions, but acting as a “reverse chemokine” by inserting its C-terminus instead of the N-terminus as in the case of chemokines into the transmembrane binding pocket of CMKLR1. These structural insights are expected to help develop synthetic analogs with therapeutic potential.

Synthesis and characterization of metal dithiocarbamate derivatives of (S)-1-phenyl-1,2,3,4-tetrahydroisoquinoline

Five metal dithiocarbamate complexes [M(PTHIQDTC)2] [where PTHIQDTC is (S)-1-phenyl-1,2,3,4-tetrahydroisoquinoline dithiocarbamate anion and M is Ni(II) (1), Sn(II) (2), Hg(II) (3), Pb(II) (4) and Zn(II) (5)] were synthesized from the reaction of MX2 (X is Cl– for 1–3 and OAc– for 4–5) with ligand of triethylammonium (S)-1-phenyl-1,2,3,4-tetrahydroisoquinoline dithiocarbamate [Et3NH][PTHIQDTC] in methanolic solution at room temperature. The five complexes were characterized by IR, 1H and13C NMR, mass spectrometry, elemental analysis and TGA analysis. Recrystallization of [Zn(PTHIQDTC)2] (5) in dimethylsulfoxide (DMSO) converts 5 to [Zn(PTHIQDTC)2(DMSO)] (6). The structure of complex 6 has been determined by X-ray crystallography. The X-ray structural analysis of 6 indicated that the zinc(II) is five-coordinated in a distorted trigonal-bipyramidal by four S atoms from two (S)-1-phenyl-1,2,3,4-tetrahydroisoquinoline dithiocarbamate anion ligands (PTHIQDTC) and one O atom from DMSO.

Probing the binding mode and interactions of proteinase K and glutathione: molecular simulation and experiments.

Proteinase K, a serine protease from Tritirachium album Limber, is crucial in research due to its potent proteolytic activity, which relies on conformational stability and substrate affinity. Glutathione (GSH), an essential intracellular antioxidant, regulates various physiological processes by interacting with proteins, influencing their stability and function. Despite the importance of both proteinase K and GSH, their potential interaction remains unexplored. Understanding this interaction could uncover new regulatory mechanisms affecting proteinase K, with significant implications for research and therapeutic applications. In this study, we systematically investigated the binding of GSH to proteinase K using a comprehensive approach in which theoretical and experimental methods mutually validate each other. Molecular docking determined the binding mode and the interaction mechanism of proteinase K and GSH. Molecular dynamics (MD) simulations revealed that GSH binding significantly improved the stability of proteinase K, affirming the binding process was spontaneous, with hydrogen bonds and van der Waals forces emerging as the predominant contributors throughout the interaction. At the same time, the fluorescence spectrum and circular dichroism spectrum confirmed the interaction mechanism between GSH and proteinase K, as well as the conformational changes of proteinase K induced by GSH binding. We believe this study could offer valuable insights for future research into the structure and binding dynamics of other protein-ligand complexes under physiological conditions.

EMGE: Entities and Mentions Gradual Enhancement with semantics and connection modelling for document-level relation extraction

Relation extraction is the process of identifying connections between entities in unstructured text and is a critical component of entity-centred information extraction to uncover latent knowledge structures in complex documents. Although graph-based methods have pushed the state-of-the-art forward in relation extraction, current approaches still exhibit limitations. These include incomplete capture of graph structural features, inadequate modelling of long-distance dependencies and imprecise representation of complex entity interactions. A novel Entities and Mentions Gradual Enhancement framework called EMGE is proposed. It integrates both contextual and structural information to robustly enhance entity representations for document-level relation extraction. It comprises three primary components: 1) a dynamic relation aware enhancement mechanism to comprehensively encode graph structural features; 2) a multi-scale feature enhancement module to effectively capture long-distance dependencies; and 3) an entity-mention pair enhancement mechanism to yield precise representations of classification targets. Extensive empirical evaluation on five widely-adopted datasets demonstrates that EMGE achieves promising performance. Particularly noteworthy are the substantial gains obtained on the challenging CDR dataset, where EMGE achieved relative improvements of 1.5%, 8.8%, and 3.5% over the strongest baseline in terms of the Intra-F1, Inter-F1 and Overall-F1 metrics, respectively. Further experimental results demonstrate that the proposed model outperforms the popular large language model in relation extraction tasks. Our code is available on github. 11EMGE: https://github.com/GZU-SAMLab/EMGE.

The influence of coordination mode differences on the structural diversity and fluorescence properties of Zn(II)/Cd(II) Schiff base complexes

Four metal complexes 1 : Zn2Cl2L2, 2 : Zn2(CH3OO)2L2·MeCN, 3 : Zn(NO3)2HL, 4 : CdCl2HL were obtained by coordinating the flexible Schiff‐base ligand 4‐amino‐N'‐(di(pyridin‐2‐yl)methylene)benzohydrazide (abbreviated as HL) with the Zn(II) and Cd(II). X‐ray single crystal diffraction confirms that the four complexes 1‐4 employ two different coordination modes. Moreover, the structures of complexes 1 and 2 are accompanied by deproton behavior, and these structural differences not only increase the fluorescence quantum yield but also produce a red shift in fluorescence emission. TD‐DFT calculations confirm that these performance changes are related to the coordination mode and coordination environment. This work not only construct the four fluorescent complexes, but also further deepen the understanding of the structure‐activity relationship between the structure of the complexes and the fluorescence properties.

Cryo-EM structure of single-layered nucleoprotein-RNA complex from Marburg virus

Marburg virus (MARV) causes lethal hemorrhagic fever in humans, posing a threat to global health. We determined by cryogenic electron microscopy (cryo-EM) the MARV helical ribonucleoprotein (RNP) complex structure in single-layered conformation, which differs from the previously reported structure of a double-layered helix. Our findings illuminate novel RNP interactions and expand knowledge on MARV genome packaging and nucleocapsid assembly, both processes representing attractive targets for the development of antiviral therapeutics against MARV disease.

Cyclometalated IrIII Complex Possessing Chiral MIC ligand: Regiospecific sp3 C-H Activation and Asymmetric Transfer Hydrogenation of Ketone.

Cyclometalation offers a wide number of organometallic metallacycles showing diverse applications. However, such NHC complexes synthesized via an sp3 C-H bond activation are rare. An iridium(III) complex with a chiral mesoionic N-heterocyclic carbene (MIC) ligand, where the IrIII forms an additional Ir-C bond via a regiospecific sp3 C-H bond activation at the N-methylbenzyl wingtip, was synthesized and characterized. To our best knowledge, this represents the first example of cyclometalated iridium(III) complex possessing a chiral MIC donor ligand. The formation of the complex was followed by 2D correlation NMR spectroscopy and the molecular formula mass was evidenced by ESI-HRMS mass spectrometry. The molecular structure of the IrIII-MIC complex was unambiguously established by the single crystal XRD data. This cyclometalated IrIII complex was employed in the asymmetric transfer hydrogenation of 4-bromoacetophenone, and the complex was successful to transfer chirality to the final alcohol molecules (up to 92% ee).

Structure of dimerized assimilatory NADPH-dependent sulfite reductase reveals the minimal interface for diflavin reductase binding.

Sulfur is one of the essential building blocks of life. Sulfur exists in numerous redox states but only one can be incorporated into biomass - S 2- (sulfide). In Escherichia coli , a protein enzyme called sulfite reductase reduces sulfite by six electrons to make sulfide. Typical electron transfer reactions move one or two electrons at a time, so this chemistry is unique. E. coli SiR is a two-protein complex composed of a diflavin reductase flavoprotein and an iron metalloenzyme hemoprotein. Until now, the molecular interactions that govern subunit interactions remained a mystery because the extreme flexibility of the flavoprotein subunit, which has challenged X-ray or cryo-EM analysis for over 30 years. In overcoming these challenges, we used a combination of rapid plunging with a high critical-micelle-concentration lipid alongside a biochemically minimized complex to determine the 2.78 Å-resolution cryo-EM structure of a dimer between the flavoprotein and hemoprotein subunits.

Wheat starch-Lonicera caerulea berry polyphenols complex regulates blood glucose and improves intestinal flora in type 2 diabetic mice

Resistant starch (RS) reduces or delays the digestion of carbohydrates and glucose synthesis, thereby lowering postprandial blood glucose levels. The wheat starch-Lonicera caerulea berry polyphenols (WS-LCBP) complex was constructed using high hydrostatic pressure (HHP). The effects of intragastric administration of WS or WS-LCBP on blood glucose in T2DM model mice. RS in the composite preparation formed by HHP and 10 % LCBP at 600 MPa for 30 min increased from 7.65 % to 49.66 %. WS–LCBP formed an A + V-type crystal structure of the polyhydroxyl non-inclusion complex, which hindered the digestion of WS into glucose. Compared with LCBP intake, which caused 8.3 % reduction in 2-h postprandial blood glucose (p < 0.05), Homeostatic model assessment for insulin resistance demonstrated a 35.3 % decrease (p < 0.001) with WS-LCBP administration. Western blotting demonstrated that exposure to WS-LCBP activated the GLP-1R/PI3K/AKT signaling pathway in the liver tissue of T2DM mice, reducing insulin resistance. Furthermore, the concentration of short-chain fatty acids was markedly elevated. The structure and abundance of the intestinal flora were enhanced. The WS-LCBP complex demonstrated a more pronounced improvement than LCBP supplementation alone. This study offers a novel perspective and theoretical foundation for the regulation of postprandial blood glucose levels by polyphenol starch-based food biomacromolecules and their potential applications in starchy foods.

Synthesis, characterization, X-ray structure, and DFT calculations of Zn complex encompassing HLN2O ligand: Relevance in cytotoxicity and antifungal photodynamic therapy.

This article presents the synthesis, characterization, and X-ray crystallographic features of one new Zn complex derived from a Salen-type tridentate ligand (HLN2O). A single-crystal diffraction study determined the complex crystal structure, which confirms that it crystallizes in the orthorhombic space group P212121. The single-crystal structure is constructed using the unique mononuclear component [ZnLN2°] and supramolecular CH∙∙∙π type interaction, resulting in a 1D structure. The IR, HRMS, and NMR study also support the complex structure. The Zn metal centre has a distorted square pyramidal geometry with τ value of 0.49. The Hirshfeld surfaces and 2D fingerprint confirm predominant H…H (77.9 %) interactions, with minor H…O, H…C, and H…N (5.0 %, 4.9 %, and 0.2 %). DFT calculations employed the B3LYP-D3/Lanl2DZ class of theory. FMO/MEP explains the complex reactivity perspective, while IP (4.71 eV) and low EA (1.11 eV) suit biological applications. The bonding gateway was analysed using NBO/QTAIM-NCI and ELF-LOL plots. Cytotoxicity was assessed using the Trypan blue exclusion method and tested against the DLA cell line, showing effectiveness against the DLA cell and suggesting complex potential as an anticancer agent. Antifungal photodynamic therapy (APDT) explored that ligand and Zn complex have significant activity against C. albicans. Finally, molecular docking simulations substantiate the experimental findings.

Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate.

Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID, toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5'-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.IMPORTANCEArchaea are one of the three domains of life, classified as a phylogenetically distinct lineage. There is a paucity of known enzyme structures from organisms of this domain, and this is often exacerbated by characteristically difficult growth conditions and a lack of readily available molecular biology toolkits to study proteins in archaeal cells. As a result, there is a gap in knowledge concerning the mechanisms governing archaeal protein behavior and their impacts on both the environment and human health; case in point, the synthesis of the widely utilized cofactor pyridoxal 5'-phosphate (PLP; a vitamer of vitamin B6, which humans cannot produce). By leveraging the power of single-particle cryo-EM and map-to-primary sequence identification, we determine the native structure of PLP synthase from cellular lysate. Our workflow allows the (i) rapid examination of new or less characterized systems with minimal sample requirements and (ii) discovery of structural states inaccessible by recombinant expression.