[English] 日本語
Yorodumi
- PDB-9sw5: Structure of the MvhAGD-HdrABC dimer of M. marburgensis under sta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9sw5
TitleStructure of the MvhAGD-HdrABC dimer of M. marburgensis under state 1 substate b (composite structure)
Components
  • (F420-non-reducing hydrogenase subunit ...) x 2
  • (H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit ...) x 3
  • F420-non-reducing hydrogenase iron-sulfur subunit D
KeywordsOXIDOREDUCTASE / hydrogenase / dehydrogenase / polyferredoxin
Function / homology
Function and homology information


Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors / H2:CoB-CoM heterodisulfide,ferredoxin reductase / CoB--CoM heterodisulfide reductase activity / methanogenesis / ferredoxin hydrogenase activity / nickel cation binding / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity ...Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors / H2:CoB-CoM heterodisulfide,ferredoxin reductase / CoB--CoM heterodisulfide reductase activity / methanogenesis / ferredoxin hydrogenase activity / nickel cation binding / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / MnmG, N-terminal domain / Glucose inhibited division protein A / CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / F420-non-reducing hydrogenase iron-sulfur subunit D / : / Methyl-viologen-reducing hydrogenase, delta subunit / Cysteine-rich domain ...: / MnmG, N-terminal domain / Glucose inhibited division protein A / CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / F420-non-reducing hydrogenase iron-sulfur subunit D / : / Methyl-viologen-reducing hydrogenase, delta subunit / Cysteine-rich domain / Cysteine-rich domain / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / 4Fe-4S dicluster domain / 4Fe-4S dicluster domain / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenase, large subunit, nickel binding site / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Alpha-helical ferredoxin / 4Fe-4S binding domain / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Non-cubane [4Fe-4S]-cluster / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Chem-NFU / IRON/SULFUR CLUSTER / F420-non-reducing hydrogenase subunit A / F420-non-reducing hydrogenase iron-sulfur subunit D / F420-non-reducing hydrogenase subunit G / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsSan Segundo-Acosta, P. / Murphy, B.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Science Advances / Year: 2026
Title: Diversity of electron-bifurcating CO2-fixing supercomplexes in methanogens
Authors: San Segundo-Acosta, P. / Nomura, S. / Fernandes-Queiroz, J.P. / Protasov, E. / Kahnt, J. / Kaneko, M. / Hochberg, G. / Shima, S. / Murphy, B.J.
History
DepositionOct 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
B: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
C: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
F: F420-non-reducing hydrogenase subunit A
E: F420-non-reducing hydrogenase subunit G
D: F420-non-reducing hydrogenase iron-sulfur subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,68422
Polymers228,9566
Non-polymers5,72816
Water181
1
A: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
B: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
C: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
F: F420-non-reducing hydrogenase subunit A
E: F420-non-reducing hydrogenase subunit G
D: F420-non-reducing hydrogenase iron-sulfur subunit D
hetero molecules

A: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
B: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
C: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
F: F420-non-reducing hydrogenase subunit A
E: F420-non-reducing hydrogenase subunit G
D: F420-non-reducing hydrogenase iron-sulfur subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)469,36944
Polymers457,91212
Non-polymers11,45732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
MethodUCSF CHIMERA

-
Components

-
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit ... , 3 types, 3 molecules ABC

#1: Protein H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A / CoB--CoM heterodisulfide reductase iron-sulfur subunit A


Mass: 72264.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: Q50756, H2:CoB-CoM heterodisulfide,ferredoxin reductase
#2: Protein H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B / CoB--CoM heterodisulfide reductase subunit B


Mass: 33496.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: Q50755, H2:CoB-CoM heterodisulfide,ferredoxin reductase
#3: Protein H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C / CoB--CoM heterodisulfide reductase iron-sulfur subunit C


Mass: 20548.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: Q50754, H2:CoB-CoM heterodisulfide,ferredoxin reductase

-
F420-non-reducing hydrogenase subunit ... , 2 types, 2 molecules FE

#4: Protein F420-non-reducing hydrogenase subunit A / Methyl viologen-reducing hydrogenase subunit alpha / MVH subunit A


Mass: 52905.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: P60227, Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors
#5: Protein F420-non-reducing hydrogenase subunit G / Methyl viologen-reducing hydrogenase subunit gamma / MVH subunit G


Mass: 33786.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: P60239, Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors

-
Protein , 1 types, 1 molecules D

#6: Protein F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl viologen-reducing hydrogenase subunit delta / MVH subunit D


Mass: 15954.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: P60238, Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors

-
Non-polymers , 6 types, 17 molecules

#7: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#9: Chemical ChemComp-9S8 / Non-cubane [4Fe-4S]-cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-NFU / formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / NI-FE REDUCED ACTIVE CENTER


Mass: 195.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3HFeN2NiO / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: FmdABCGF region of the (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme of M. marburgensis
Type: COMPLEX / Entity ID: #1, #6, #5, #2-#4 / Source: NATURAL
Molecular weightValue: 1.2 MDa / Experimental value: YES
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Buffer solutionpH: 7.6
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The buffer is pH 7.6 100 mM sodium phosphate with 150 mM NaCl, and containing 2 mM DTT
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 700 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.55 sec. / Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 18777
EM imaging opticsEnergyfilter name: TFS Selectris X

-
Processing

EM software
IDNameCategory
1RELIONparticle selection
2EPUimage acquisition
7UCSF ChimeraXmodel fitting
9Cootmodel refinement
10RELIONinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 917008
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17398 / Details: Particles had been C2-symmetry expanded / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingDetails: Generated using ModelAngelo / Source name: Other / Type: other
RefinementHighest resolution: 3.29 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00823248
ELECTRON MICROSCOPYf_angle_d0.69431584
ELECTRON MICROSCOPYf_dihedral_angle_d3.9453129
ELECTRON MICROSCOPYf_chiral_restr0.0413535
ELECTRON MICROSCOPYf_plane_restr0.0034058

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more