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- PDB-6cfw: cryoEM structure of a respiratory membrane-bound hydrogenase -

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Entry
Database: PDB / ID: 6cfw
TitlecryoEM structure of a respiratory membrane-bound hydrogenase
Components
  • (MBH subunit) x 3
  • (Membrane-bound hydrogenase subunit ...) x 2
  • (Monovalent cation/H+ antiporter subunit ...) x 6
  • Mbh13 NADH dehydrogenase subunit
  • NADH-plastoquinone oxidoreductase subunit
  • Probable membrane-bound hydrogenase subunit mbhJ
KeywordsMEMBRANE PROTEIN / respiratory / hydrogenase / ion translocation
Function / homology
Function and homology information


ferredoxin hydrogenase / sodium:proton antiporter activity / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / monoatomic cation transmembrane transporter activity / oxidoreductase activity, acting on NAD(P)H / proton motive force-driven ATP synthesis / nickel cation binding / NADH dehydrogenase (ubiquinone) activity / quinone binding ...ferredoxin hydrogenase / sodium:proton antiporter activity / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / monoatomic cation transmembrane transporter activity / oxidoreductase activity, acting on NAD(P)H / proton motive force-driven ATP synthesis / nickel cation binding / NADH dehydrogenase (ubiquinone) activity / quinone binding / NAD binding / 4 iron, 4 sulfur cluster binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
: / : / : / MrpA C-terminal/MbhE / : / : / MBH, subunit E / Na+/H+ antiporter subunit E / Na+/H+ antiporter subunit G / Na+/H+ antiporter MnhB subunit-related protein ...: / : / : / MrpA C-terminal/MbhE / : / : / MBH, subunit E / Na+/H+ antiporter subunit E / Na+/H+ antiporter subunit G / Na+/H+ antiporter MnhB subunit-related protein / Na(+)/H(+) antiporter subunit F-like / MrpA C-terminal/MbhD / : / Na+/H+ ion antiporter subunit / Na+/H+ antiporter subunit / Domain related to MnhB subunit of Na+/H+ antiporter / Multiple resistance and pH regulation protein F (MrpF / PhaF) / MBH, subunit D / 4Fe-4S dicluster domain / Rossmann fold - #12280 / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / NADH-quinone oxidoreductase, chain I / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NFU / IRON/SULFUR CLUSTER / Monovalent cation/H+ antiporter subunit E / Monovalent cation/H+ antiporter subunit B / Hydrogenase / NADH-plastoquinone oxidoreductase subunit / Monovalent cation/H+ antiporter subunit G / Monovalent cation/H+ antiporter subunit D / Mbh13 NADH dehydrogenase subunit / Monovalent cation/H+ antiporter subunit F ...Chem-NFU / IRON/SULFUR CLUSTER / Monovalent cation/H+ antiporter subunit E / Monovalent cation/H+ antiporter subunit B / Hydrogenase / NADH-plastoquinone oxidoreductase subunit / Monovalent cation/H+ antiporter subunit G / Monovalent cation/H+ antiporter subunit D / Mbh13 NADH dehydrogenase subunit / Monovalent cation/H+ antiporter subunit F / Monovalent cation/H+ antiporter subunit C / MrpA C-terminal/MbhE domain-containing protein / Membrane-bound hydrogenase subunit alpha / Membrane-bound hydrogenase subunit beta / Probable membrane-bound hydrogenase subunit mbhJ / MrpA C-terminal/MbhD domain-containing protein
Similarity search - Component
Biological speciesPyrococcus furiosus COM1 (archaea)
Pyrococcus furiosus (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLi, H.L. / Yu, H.J.
CitationJournal: Cell / Year: 2018
Title: Structure of an Ancient Respiratory System.
Authors: Hongjun Yu / Chang-Hao Wu / Gerrit J Schut / Dominik K Haja / Gongpu Zhao / John W Peters / Michael W W Adams / Huilin Li /
Abstract: Hydrogen gas-evolving membrane-bound hydrogenase (MBH) and quinone-reducing complex I are homologous respiratory complexes with a common ancestor, but a structural basis for their evolutionary ...Hydrogen gas-evolving membrane-bound hydrogenase (MBH) and quinone-reducing complex I are homologous respiratory complexes with a common ancestor, but a structural basis for their evolutionary relationship is lacking. Here, we report the cryo-EM structure of a 14-subunit MBH from the hyperthermophile Pyrococcus furiosus. MBH contains a membrane-anchored hydrogenase module that is highly similar structurally to the quinone-binding Q-module of complex I while its membrane-embedded ion-translocation module can be divided into a H- and a Na-translocating unit. The H-translocating unit is rotated 180° in-membrane with respect to its counterpart in complex I, leading to distinctive architectures for the two respiratory systems despite their largely conserved proton-pumping mechanisms. The Na-translocating unit, absent in complex I, resembles that found in the Mrp H/Na antiporter and enables hydrogen gas evolution by MBH to establish a Na gradient for ATP synthesis near 100°C. MBH also provides insights into Mrp structure and evolution of MBH-based respiratory enzymes.
History
DepositionFeb 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.0May 23, 2018Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 23, 2018Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 23, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 23, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 23, 2018Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 23, 2018Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 23, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 23, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 23, 2018Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 23, 2018Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 23, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 23, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 23, 2018Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 23, 2018Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 23, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 23, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Dec 18, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 14, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
H: Monovalent cation/H+ antiporter subunit D
G: Monovalent cation/H+ antiporter subunit C
D: MBH subunit
I: MBH subunit
M: Mbh13 NADH dehydrogenase subunit
F: Monovalent cation/H+ antiporter subunit B
A: Monovalent cation/H+ antiporter subunit E
E: MBH subunit
C: Monovalent cation/H+ antiporter subunit G
B: Monovalent cation/H+ antiporter subunit F
J: Probable membrane-bound hydrogenase subunit mbhJ
K: Membrane-bound hydrogenase subunit beta
L: Membrane-bound hydrogenase subunit alpha
N: NADH-plastoquinone oxidoreductase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,21618
Polymers291,96614
Non-polymers1,2514
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Monovalent cation/H+ antiporter subunit ... , 6 types, 6 molecules HGFACB

#1: Protein Monovalent cation/H+ antiporter subunit D


Mass: 55016.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06375 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6UQL5
#2: Protein Monovalent cation/H+ antiporter subunit C


Mass: 12784.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06370 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6UZU1
#6: Protein Monovalent cation/H+ antiporter subunit B


Mass: 15531.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06365 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6TXN5
#7: Protein Monovalent cation/H+ antiporter subunit E


Mass: 18750.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06340 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6TXN1
#9: Protein Monovalent cation/H+ antiporter subunit G


Mass: 13521.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06350 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6UQL1
#10: Protein Monovalent cation/H+ antiporter subunit F


Mass: 9063.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06345 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6UZT7

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Protein , 6 types, 6 molecules DIMEJN

#3: Protein MBH subunit


Mass: 10423.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1426 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: Q8U104
#4: Protein MBH subunit


Mass: 13055.353 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06380 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6U847
#5: Protein Mbh13 NADH dehydrogenase subunit


Mass: 35414.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06400 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6UQM0
#8: Protein MBH subunit


Mass: 11149.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06360 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6V287
#11: Protein Probable membrane-bound hydrogenase subunit mbhJ


Mass: 18324.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: mbhJ, mbh10, PF1432 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: Q8U0Z8, ferredoxin hydrogenase
#14: Protein NADH-plastoquinone oxidoreductase subunit


Mass: 15707.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06405 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6U851

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Membrane-bound hydrogenase subunit ... , 2 types, 2 molecules KL

#12: Protein Membrane-bound hydrogenase subunit beta


Mass: 20213.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: mbhK, mbh11, PF1433 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: Q8U0Z7, ferredoxin hydrogenase
#13: Protein Membrane-bound hydrogenase subunit alpha / MBH-alpha


Mass: 43008.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: mbhL, mbh12, PF1434 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: Q8U0Z6, ferredoxin hydrogenase

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Non-polymers , 2 types, 4 molecules

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


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#16: 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

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Details

Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Membrane-bound Hydrogenase (MBH) complex / Type: COMPLEX / Entity ID: #1-#14 / Source: RECOMBINANT
Source (natural)Organism: Pyrococcus furiosus (archaea)
Source (recombinant)Organism: Pyrococcus furiosus (archaea)
Buffer solutionpH: 8.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
4CTFFIND4CTF correction
8PHENIXmodel refinement
13RELION23D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131679 / Symmetry type: POINT
RefinementHighest resolution: 3.7 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0120064
ELECTRON MICROSCOPYf_angle_d1.28727315
ELECTRON MICROSCOPYf_dihedral_angle_d12.90711798
ELECTRON MICROSCOPYf_chiral_restr0.0693212
ELECTRON MICROSCOPYf_plane_restr0.0113363

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