7BKB

Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (hexameric, composite structure)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Three-megadalton complex of methanogenic electron-bifurcating and CO 2 -fixing enzymes.

Watanabe, T.Pfeil-Gardiner, O.Kahnt, J.Koch, J.Shima, S.Murphy, B.J.

(2021) Science 373: 1151-1156

  • DOI: https://doi.org/10.1126/science.abg5550
  • Primary Citation of Related Structures:  
    7BKB, 7BKC, 7BKD, 7BKE

  • PubMed Abstract: 

    The first reaction of the methanogenic pathway from carbon dioxide (CO 2 ) is the reduction and condensation of CO 2 to formyl-methanofuran, catalyzed by formyl-methanofuran dehydrogenase (Fmd). Strongly reducing electrons for this reaction are generated by heterodisulfide reductase (Hdr) in complex with hydrogenase or formate dehydrogenase (Fdh) using a flavin-based electron-bifurcation mechanism. Here, we report enzymological and structural characterizations of Fdh-Hdr-Fmd complexes from Methanospirillum hungatei . The complexes catalyze this reaction using electrons from formate and the reduced form of the electron carrier F 420 . Conformational changes in HdrA mediate electron bifurcation, and polyferredoxin FmdF directly transfers electrons to the CO 2 reduction site, as evidenced by methanofuran-dependent flavin-based electron bifurcation even without free ferredoxin, a diffusible electron carrier between Hdr and Fmd. Conservation of Hdr and Fmd structures suggests that this complex is common among hydrogenotrophic methanogens.


  • Organizational Affiliation

    Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CoB--CoM heterodisulfide reductase iron-sulfur subunit AA,
M [auth a]
671Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.8
UniProt
Find proteins for Q2FKZ1 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
Explore Q2FKZ1 
Go to UniProtKB:  Q2FKZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FKZ1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
F420-non-reducing hydrogenase subunit DB [auth F],
N [auth f]
140Methanospirillum hungatei JF-1Mutation(s): 0 
UniProt
Find proteins for Q2FKZ0 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
Explore Q2FKZ0 
Go to UniProtKB:  Q2FKZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FKZ0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase, beta subunit (F420)C [auth E],
O [auth e]
414Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.2.99
UniProt
Find proteins for Q2FME3 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
Explore Q2FME3 
Go to UniProtKB:  Q2FME3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FME3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CoB--CoM heterodisulfide reductase subunit CD [auth C],
P [auth c]
191Methanospirillum hungatei JF-1Mutation(s): 0 
UniProt
Find proteins for Q2FKZ3 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
Explore Q2FKZ3 
Go to UniProtKB:  Q2FKZ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FKZ3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CoB--CoM heterodisulfide reductase subunit BE [auth B],
Q [auth b]
296Methanospirillum hungatei JF-1Mutation(s): 0 
UniProt
Find proteins for Q2FKZ2 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
Explore Q2FKZ2 
Go to UniProtKB:  Q2FKZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FKZ2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenaseF [auth D],
R [auth d]
686Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.17.1.9
UniProt
Find proteins for Q2FRK1 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
Explore Q2FRK1 
Go to UniProtKB:  Q2FRK1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FRK1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenaseG [auth I],
S [auth i]
266Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.2.7.12
UniProt
Find proteins for Q2FRL8 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
Explore Q2FRL8 
Go to UniProtKB:  Q2FRL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FRL8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenase, subunit GH [auth L],
T [auth l]
146Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.2.99.5
UniProt
Find proteins for Q2FKZ5 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
Explore Q2FKZ5 
Go to UniProtKB:  Q2FKZ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FKZ5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenase, subunit AI [auth G],
U [auth g]
571Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.2.99.5
UniProt
Find proteins for Q2FRL9 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
Explore Q2FRL9 
Go to UniProtKB:  Q2FRL9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FRL9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenase, subunit DJ,
V [auth j]
137Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.2.99.5
UniProt
Find proteins for Q2FRF6 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
Explore Q2FRF6 
Go to UniProtKB:  Q2FRF6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FRF6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenase, subunit FK,
W [auth k]
388Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.2.99.5
UniProt
Find proteins for Q2FKZ4 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
Explore Q2FKZ4 
Go to UniProtKB:  Q2FKZ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FKZ4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenase, subunit BL [auth H],
X [auth h]
443Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.2.99.5
UniProt
Find proteins for Q2FRM0 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
Explore Q2FRM0 
Go to UniProtKB:  Q2FRM0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FRM0
Sequence Annotations
Expand
  • 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 
HB [auth a],
KA [auth E],
SB [auth e],
Z [auth A]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MGD (Subject of Investigation/LOI)
Query on MGD

Download Ideal Coordinates CCD File 
DB [auth H],
EB [auth H],
LC [auth h],
MC [auth h]
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
SF4
Query on SF4

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth K]
BA [auth A]
BB [auth K]
CA [auth A]
AA [auth A],
AB [auth K],
BA [auth A],
BB [auth K],
CA [auth A],
CC [auth k],
DA [auth A],
DC [auth k],
EA [auth A],
EC [auth k],
FB [auth H],
FC [auth k],
GA [auth E],
GB [auth a],
GC [auth k],
HA [auth E],
HC [auth k],
IA [auth E],
IB [auth a],
IC [auth k],
JA [auth E],
JB [auth a],
JC [auth k],
KB [auth a],
LA [auth C],
LB [auth a],
MA [auth C],
MB [auth a],
NC [auth h],
OB [auth e],
PA [auth D],
PB [auth e],
QA [auth L],
QB [auth e],
RA [auth L],
RB [auth e],
TB [auth c],
UA [auth K],
UB [auth c],
VA [auth K],
WA [auth K],
XA [auth K],
XB [auth d],
Y [auth A],
YA [auth K],
YB [auth l],
ZA [auth K],
ZB [auth l]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
9S8 (Subject of Investigation/LOI)
Query on 9S8

Download Ideal Coordinates CCD File 
NA [auth B],
OA [auth B],
VB [auth b],
WB [auth b]
Non-cubane [4Fe-4S]-cluster
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
FA [auth F],
NB [auth f]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MO
Query on MO

Download Ideal Coordinates CCD File 
CB [auth H],
KC [auth h]
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AC [auth g],
BC [auth g],
SA [auth G],
TA [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
I [auth G],
U [auth g]
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
German Research Foundation (DFG)GermanySH 87/1-1
Japan Society for the Promotion of Science (JSPS)Japan--
Alexander von Humboldt FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release