6TGA

Cryo-EM Structure of as isolated form of NAD+-dependent Formate Dehydrogenase from Rhodobacter capsulatus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase.

Radon, C.Mittelstadt, G.Duffus, B.R.Burger, J.Hartmann, T.Mielke, T.Teutloff, C.Leimkuhler, S.Wendler, P.

(2020) Nat Commun 11: 1912-1912

  • DOI: https://doi.org/10.1038/s41467-020-15614-0
  • Primary Citation of Related Structures:  
    6TG9, 6TGA

  • PubMed 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 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.


  • Organizational Affiliation

    Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476, Potsdam-Golm, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase subunit alpha
A, E
958Rhodobacter capsulatusMutation(s): 0 
Gene Names: U715_16550
UniProt
Find proteins for D5AQH0 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Explore D5AQH0 
Go to UniProtKB:  D5AQH0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5AQH0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase subunit beta
B, F
500Rhodobacter capsulatusMutation(s): 0 
Gene Names: U715_16555
UniProt
Find proteins for D5AQH1 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Explore D5AQH1 
Go to UniProtKB:  D5AQH1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5AQH1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase subunit gammaC [auth G],
G [auth C]
150Rhodobacter capsulatusMutation(s): 0 
Gene Names: U715_16560
EC: 1.2.1.2
UniProt
Find proteins for D5AQH2 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Explore D5AQH2 
Go to UniProtKB:  D5AQH2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5AQH2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent formate dehydrogenase subunit delta
D, H
71Rhodobacter capsulatusMutation(s): 0 
Gene Names: U715_16540
UniProt
Find proteins for D5AQG8 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Explore D5AQG8 
Go to UniProtKB:  D5AQG8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5AQG8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGD (Subject of Investigation/LOI)
Query on MGD

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
U [auth E],
V [auth E]
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
DA [auth F],
R [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
EA [auth F]
M [auth A]
N [auth A]
AA [auth E],
BA [auth E],
EA [auth F],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
S [auth B],
Y [auth E],
Z [auth E]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
FA [auth C],
L [auth A],
T [auth G],
X [auth E]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
6MO (Subject of Investigation/LOI)
Query on 6MO

Download Ideal Coordinates CCD File 
K [auth A],
W [auth E]
MOLYBDENUM(VI) ION
Mo
HCNGUXXTNNIKCQ-UHFFFAOYSA-N
H2S (Subject of Investigation/LOI)
Query on H2S

Download Ideal Coordinates CCD File 
CA [auth E],
Q [auth A]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.14

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyEXC 314/2
German Research FoundationGermanyEXC 2008/1
European UnionGermanyiNext-4008

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references