6CFW

cryoEM structure of a respiratory membrane-bound hydrogenase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of an Ancient Respiratory System.

Yu, H.Wu, C.H.Schut, G.J.Haja, D.K.Zhao, G.Peters, J.W.Adams, M.W.W.Li, H.

(2018) Cell 173: 1636

  • DOI: 10.1016/j.cell.2018.03.071
  • Primary Citation of Related Structures:  
    6CFW

  • PubMed 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 relationship is lacking. Here, we report the cryo-EM structure of a 14-subunit MBH from the hyperthermophile Pyrococcus furiosus ...

    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.


    Organizational Affiliation

    Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI 49503, USA. Electronic address: huilin.li@vai.org.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Monovalent cation/H+ antiporter subunit DA [auth H]510Pyrococcus furiosus COM1Mutation(s): 0 
Gene Names: PFC_06375
Membrane Entity: Yes 
UniProt
Find proteins for I6UQL5 (Pyrococcus furiosus COM1)
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UniProt GroupI6UQL5
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Monovalent cation/H+ antiporter subunit CB [auth G]117Pyrococcus furiosus COM1Mutation(s): 0 
Gene Names: PFC_06370
Membrane Entity: Yes 
UniProt
Find proteins for I6UZU1 (Pyrococcus furiosus COM1)
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UniProt GroupI6UZU1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MBH subunitC [auth D]96Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: PF1426
Membrane Entity: Yes 
UniProt
Find proteins for Q8U104 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
MBH subunitD [auth I]115Pyrococcus furiosus COM1Mutation(s): 0 
Gene Names: PFC_06380
Membrane Entity: Yes 
UniProt
Find proteins for I6U847 (Pyrococcus furiosus COM1)
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UniProt GroupI6U847
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Mbh13 NADH dehydrogenase subunitE [auth M]321Pyrococcus furiosus COM1Mutation(s): 0 
Gene Names: PFC_06400
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Monovalent cation/H+ antiporter subunit BF148Pyrococcus furiosus COM1Mutation(s): 0 
Gene Names: PFC_06365
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Monovalent cation/H+ antiporter subunit EG [auth A]167Pyrococcus furiosus COM1Mutation(s): 0 
Gene Names: PFC_06340
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
MBH subunitH [auth E]99Pyrococcus furiosus COM1Mutation(s): 0 
Gene Names: PFC_06360
Membrane Entity: Yes 
UniProt
Find proteins for I6V287 (Pyrococcus furiosus COM1)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Monovalent cation/H+ antiporter subunit GI [auth C]124Pyrococcus furiosus COM1Mutation(s): 0 
Gene Names: PFC_06350
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Monovalent cation/H+ antiporter subunit FJ [auth B]84Pyrococcus furiosus COM1Mutation(s): 0 
Gene Names: PFC_06345
Membrane Entity: Yes 
UniProt
Find proteins for I6UZT7 (Pyrococcus furiosus COM1)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Probable membrane-bound hydrogenase subunit mbhJK [auth J]167Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: mbhJmbh10PF1432
EC: 1.12.7.2
Membrane Entity: Yes 
UniProt
Find proteins for Q8U0Z8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Membrane-bound hydrogenase subunit betaL [auth K]173Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: mbhKmbh11PF1433
EC: 1.12.7.2
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Membrane-bound hydrogenase subunit alphaM [auth L]380Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: mbhLmbh12PF1434
EC: 1.12.7.2
Membrane Entity: Yes 
UniProt
Find proteins for Q8U0Z6 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-plastoquinone oxidoreductase subunitN139Pyrococcus furiosus COM1Mutation(s): 0 
Gene Names: PFC_06405
UniProt
Find proteins for I6U851 (Pyrococcus furiosus COM1)
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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O [auth J],
Q [auth N],
R [auth N]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
NFU
Query on NFU

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P [auth L]formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)
C3 H Fe N2 Ni O
QCZROEOIPZWDEO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2018-02-17 
  • Released Date: 2018-05-23 
  • Deposition Author(s): Li, H.L., Yu, H.J.

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2018-06-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Other