6TG9

Cryo-EM Structure of NADH reduced form of NAD+-dependent Formate Dehydrogenase from Rhodobacter capsulatus

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase subunit alpha
A, E
958Rhodobacter capsulatus Y262Mutation(s): 0 
Gene Names: U715_16550
EC: 1.17.1.9
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 capsulatus Y262Mutation(s): 0 
Gene Names: U715_16555
EC: 1.2.1.2
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 capsulatus Y262Mutation(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 capsulatus Y262Mutation(s): 0 
Gene Names: U715_16540
EC: 1.2.1.2
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 7 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],
V [auth E],
W [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
NAI (Subject of Investigation/LOI)
Query on NAI
Download Ideal Coordinates CCD File 
GA [auth F],
T [auth B]		1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
FMN (Subject of Investigation/LOI)
Query on FMN
Download Ideal Coordinates CCD File 
EA [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]
CA [auth E]
FA [auth F]
M [auth A]
AA [auth E],
BA [auth E],
CA [auth E],
FA [auth F],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
S [auth B],
Z [auth E]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES
Download Ideal Coordinates CCD File 
HA [auth C],
L [auth A],
U [auth G],
Y [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],
X [auth E]		MOLYBDENUM(VI) ION
Mo
HCNGUXXTNNIKCQ-UHFFFAOYSA-N
H2S (Subject of Investigation/LOI)
Query on H2S
Download Ideal Coordinates CCD File 
DA [auth E],
Q [auth A]		HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.14

Structure Validation

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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
  • Version 1.2: 2024-05-22
    Changes: Data collection, Database references, Derived calculations, Refinement description