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Yorodumi- PDB-6tg9: Cryo-EM Structure of NADH reduced form of NAD+-dependent Formate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tg9 | ||||||||||||
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Title | Cryo-EM Structure of NADH reduced form of NAD+-dependent Formate Dehydrogenase from Rhodobacter capsulatus | ||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / molybdoenzyme / formate oxidation / NAD+-dependent | ||||||||||||
Function / homology | Function and homology information formate dehydrogenase complex / formate dehydrogenase / formate metabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase complex / molybdopterin cofactor binding / cellular respiration / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding ...formate dehydrogenase complex / formate dehydrogenase / formate metabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase complex / molybdopterin cofactor binding / cellular respiration / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Rhodobacter capsulatus (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å | ||||||||||||
Authors | Wendler, P. / Radon, C. / Mittelstaedt, G. | ||||||||||||
Funding support | Germany, 3items
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Citation | Journal: Nat Commun / Year: 2020 Title: Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase. Authors: Christin Radon / Gerd Mittelstädt / Benjamin R Duffus / Jörg Bürger / Tobias Hartmann / Thorsten Mielke / Christian Teutloff / Silke Leimkühler / Petra Wendler / Abstract: Metal-containing formate dehydrogenases (FDH) catalyse the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active site. They display a diverse subunit and cofactor ...Metal-containing formate dehydrogenases (FDH) catalyse the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active site. They display a diverse subunit and cofactor composition, but structural information on these enzymes is limited. Here we report the cryo-electron microscopic structures of the soluble Rhodobacter capsulatus FDH (RcFDH) as isolated and in the presence of reduced nicotinamide adenine dinucleotide (NADH). RcFDH assembles into a 360 kDa dimer of heterotetramers revealing a putative interconnection of electron pathway chains. In the presence of NADH, the RcFDH structure shows charging of cofactors, indicative of an increased electron load. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6tg9.cif.gz | 571 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tg9.ent.gz | 460.8 KB | Display | PDB format |
PDBx/mmJSON format | 6tg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tg9_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6tg9_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6tg9_validation.xml.gz | 97.7 KB | Display | |
Data in CIF | 6tg9_validation.cif.gz | 146.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/6tg9 ftp://data.pdbj.org/pub/pdb/validation_reports/tg/6tg9 | HTTPS FTP |
-Related structure data
Related structure data | 10495MC 6tgaC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Formate dehydrogenase subunit ... , 3 types, 6 molecules AEBFGC
#1: Protein | Mass: 104589.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: U715_16550 / Production host: Rhodobacter capsulatus (bacteria) / References: UniProt: A0A0E2PAE3, UniProt: D5AQH0*PLUS #2: Protein | Mass: 52755.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: U715_16555 / Production host: Rhodobacter capsulatus (bacteria) / References: UniProt: A0A0E2P9P2, UniProt: D5AQH1*PLUS #3: Protein | Mass: 15603.050 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: U715_16560 / Production host: Rhodobacter capsulatus (bacteria) References: UniProt: A0A0E2PAI9, UniProt: D5AQH2*PLUS, formate dehydrogenase |
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-Protein , 1 types, 2 molecules DH
#4: Protein | Mass: 7388.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: U715_16540 / Production host: Rhodobacter capsulatus (bacteria) / References: UniProt: A0A0E2P9Z0, UniProt: D5AQG8*PLUS |
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-Non-polymers , 7 types, 26 molecules
#5: Chemical | ChemComp-MGD / #6: Chemical | #7: Chemical | ChemComp-FES / #8: Chemical | ChemComp-SF4 / #9: Chemical | #10: Chemical | #11: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Formate dehydrogenase, NADH reduced / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT | ||||||||||||
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Molecular weight | Value: 0.36 MDa / Experimental value: YES | ||||||||||||
Source (natural) | Organism: Rhodobacter capsulatus (bacteria) | ||||||||||||
Source (recombinant) | Organism: Rhodobacter capsulatus (bacteria) | ||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||
Buffer component |
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Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/4 | ||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company / Model: Titan Krios / Image courtesy: FEI Company | |||||||||||||||
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EM imaging | Accelerating voltage: 300 kV / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Mode: BRIGHT FIELD / Specimen-ID: 1
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Image recording |
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-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Details: CTFFIND4 was used to estimate contrast transfer function parameters. CTF correction was done in Relion 3.0. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 199229 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Highest resolution: 3.24 Å | ||||||||||||||||||||||||||||
Refine LS restraints |
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