8OH5 | pdb_00008oh5

Cryo-EM structure of the electron bifurcating transhydrogenase StnABC complex from Sporomusa Ovata (state 2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8OH5

This is version 1.2 of the entry. See complete history

Literature

Molecular architecture and electron transfer pathway of the Stn family transhydrogenase.

Kumar, A.Kremp, F.Roth, J.Freibert, S.A.Muller, V.Schuller, J.M.

(2023) Nat Commun 14: 5484-5484

  • DOI: https://doi.org/10.1038/s41467-023-41212-x
  • Primary Citation Related Structures: 
    8OH5, 8OH9

  • PubMed Abstract: 

    The challenge of endergonic reduction of NADP + using NADH is overcome by ferredoxin-dependent transhydrogenases that employ electron bifurcation for electron carrier adjustments in the ancient Wood-Ljungdahl pathway. Recently, an electron-bifurcating transhydrogenase with subunit compositions distinct from the well-characterized Nfn-type transhydrogenase was described: the Stn complex. Here, we present the single-particle cryo-EM structure of the Stn family transhydrogenase from the acetogenic bacterium Sporomusa ovata and functionally dissect its electron transfer pathway. Stn forms a tetramer consisting of functional heterotrimeric StnABC complexes. Our findings demonstrate that the StnAB subunits assume the structural and functional role of a bifurcating module, homologous to the HydBC core of the electron-bifurcating HydABC complex. Moreover, StnC contains a NuoG-like domain and a GltD-like NADPH binding domain that resembles the NfnB subunit of the NfnAB complex. However, in contrast to NfnB, StnC lost the ability to bifurcate electrons. Structural comparison allows us to describe how the same fold on one hand evolved bifurcation activity on its own while on the other hand combined with an associated bifurcating module, exemplifying modular evolution in anaerobic metabolism to produce activities critical for survival at the thermodynamic limit of life.


  • Organizational Affiliation
    • SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 861.76 kDa 
  • Atom Count: 58,624 
  • Modeled Residue Count: 7,624 
  • Deposited Residue Count: 7,736 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NAD-dependent formate dehydrogenase gamma subunit
A, D, G, J
178Sporomusa ovata DSM 2662Mutation(s): 0 
UniProt
Find proteins for A0A0U1KYW8 (Sporomusa ovata)
Explore A0A0U1KYW8 
Go to UniProtKB:  A0A0U1KYW8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U1KYW8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NAD-reducing hydrogenase subunit HoxF
B, E, H, K
584Sporomusa ovata DSM 2662Mutation(s): 0 
EC: 1.12.1.2
UniProt
Find proteins for A0A0U1KYM9 (Sporomusa ovata)
Explore A0A0U1KYM9 
Go to UniProtKB:  A0A0U1KYM9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U1KYM9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Formate dehydrogenase-O, major subunit
C, F, I, L
1,172Sporomusa ovata DSM 2662Mutation(s): 0 
EC: 1.2.1.2
UniProt
Find proteins for A0A0U1KYI6 (Sporomusa ovata)
Explore A0A0U1KYI6 
Go to UniProtKB:  A0A0U1KYI6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U1KYI6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
(Subject of Investigation/LOI)

Query on FAD



Download:Ideal Coordinates CCD File
CB [auth I],
LA [auth F],
TB [auth L],
U [auth C]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
NDP
(Subject of Investigation/LOI)

Query on NDP



Download:Ideal Coordinates CCD File
EB [auth I],
NA [auth F],
VB [auth L],
W [auth C]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
NAD
(Subject of Investigation/LOI)

Query on NAD



Download:Ideal Coordinates CCD File
AB [auth H],
JA [auth E],
RB [auth K],
S [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
FMN
(Subject of Investigation/LOI)

Query on FMN



Download:Ideal Coordinates CCD File
GA [auth E],
OB [auth K],
P [auth B],
XA [auth H]
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 C]
AC [auth L]
BA [auth C]
BB [auth H]
DB [auth I]
AA [auth C],
AC [auth L],
BA [auth C],
BB [auth H],
DB [auth I],
FB [auth I],
GB [auth I],
HA [auth E],
HB [auth I],
IA [auth E],
IB [auth I],
JB [auth I],
KA [auth E],
MA [auth F],
OA [auth F],
PA [auth F],
PB [auth K],
Q [auth B],
QA [auth F],
QB [auth K],
R [auth B],
RA [auth F],
SA [auth F],
SB [auth K],
T [auth B],
UB [auth L],
V [auth C],
WB [auth L],
X [auth C],
XB [auth L],
Y [auth C],
YA [auth H],
YB [auth L],
Z [auth C],
ZA [auth H],
ZB [auth L]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
(Subject of Investigation/LOI)

Query on FES



Download:Ideal Coordinates CCD File
BC [auth L]
CA [auth C]
DA [auth D]
FA [auth E]
KB [auth I]
BC [auth L],
CA [auth C],
DA [auth D],
FA [auth E],
KB [auth I],
LB [auth J],
M [auth A],
NB [auth K],
O [auth B],
TA [auth F],
UA [auth G],
WA [auth H]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
EA [auth E],
MB [auth K],
N [auth B],
VA [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union101075992
German Research Foundation (DFG)GermanySCHU 3364/1-1

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Database references
  • Version 1.2: 2025-10-01
    Changes: Advisory, Data collection, Derived calculations, Structure summary