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- EMDB-7468: cryoEM structure of a respiratory membrane-bound hydrogenase -

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Basic information

Entry
Database: EMDB / ID: EMD-7468
TitlecryoEM structure of a respiratory membrane-bound hydrogenase
Map datacryoEM structure of a respiratory membrane-bound hydrogenase
Sample
  • Complex: Membrane-bound Hydrogenase (MBH) complex
    • Protein or peptide: x 14 types
  • Ligand: x 2 types
Keywordsrespiratory / hydrogenase / ion translocation / MEMBRANE PROTEIN
Function / homology
Function and homology information


: / monoatomic ion transmembrane transporter activity / ferredoxin hydrogenase / 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 ...: / monoatomic ion transmembrane transporter activity / ferredoxin hydrogenase / 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 / membrane => GO:0016020 / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / 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) ...: / 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 / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / NADH-quinone oxidoreductase, chain I / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / 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
Similarity search - Domain/homology
Monovalent cation/H+ antiporter subunit E / Monovalent cation/H+ antiporter subunit B / Uncharacterized protein / 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 / Uncharacterized protein ...Monovalent cation/H+ antiporter subunit E / Monovalent cation/H+ antiporter subunit B / Uncharacterized protein / 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 / Uncharacterized protein / Membrane-bound hydrogenase subunit alpha / Membrane-bound hydrogenase subunit beta / Probable membrane-bound hydrogenase subunit mbhJ / DUF4040 domain-containing protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea) / Pyrococcus furiosus COM1 (archaea) / Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLi HL / Yu HJ
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, 2018-
Header (metadata) releaseMar 28, 2018-
Map releaseMay 23, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.048
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.048
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6cfw
  • Surface level: 0.048
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7468.png

Downloads & links

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Map

FileDownload / File: emd_7468.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcryoEM structure of a respiratory membrane-bound hydrogenase
Voxel sizeX=Y=Z: 1.088 Å
Density
Contour LevelBy AUTHOR: 0.048 / Movie #1: 0.048
Minimum - Maximum-0.113098 - 0.41419628
Average (Standard dev.)0.00042001432 (±0.007947552)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 304.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0881.0881.088
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z304.640304.640304.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ242496
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1130.4140.000

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Supplemental data

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Sample components

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Entire : Membrane-bound Hydrogenase (MBH) complex

EntireName: Membrane-bound Hydrogenase (MBH) complex
Components
  • Complex: Membrane-bound Hydrogenase (MBH) complex
    • Protein or peptide: Monovalent cation/H+ antiporter subunit D
    • Protein or peptide: Monovalent cation/H+ antiporter subunit C
    • Protein or peptide: MBH subunit
    • Protein or peptide: MBH subunit
    • Protein or peptide: Mbh13 NADH dehydrogenase subunit
    • Protein or peptide: Monovalent cation/H+ antiporter subunit B
    • Protein or peptide: Monovalent cation/H+ antiporter subunit E
    • Protein or peptide: MBH subunit
    • Protein or peptide: Monovalent cation/H+ antiporter subunit G
    • Protein or peptide: Monovalent cation/H+ antiporter subunit F
    • Protein or peptide: Probable membrane-bound hydrogenase subunit mbhJ
    • Protein or peptide: Membrane-bound hydrogenase subunit beta
    • Protein or peptide: Membrane-bound hydrogenase subunit alpha
    • Protein or peptide: NADH-plastoquinone oxidoreductase subunit
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)

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Supramolecule #1: Membrane-bound Hydrogenase (MBH) complex

SupramoleculeName: Membrane-bound Hydrogenase (MBH) complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Pyrococcus furiosus (archaea)

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

MacromoleculeName: Monovalent cation/H+ antiporter subunit D / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 55.016523 KDa
Recombinant expressionOrganism: Pyrococcus furiosus (archaea)
SequenceString: MTWLPFIIII PLLGAFSMPI VSLLKGKAKE IWASMISFAT LIVGIQVFRE VWSKGTIVYT LGAPNPFGKA TFPIRIVWEV DKFGALMVL IVTFVSFLAV IYSIEYMKHD TGLEKFYTLI LILELGMLGI AITGDIFNFY VFLEIMSIAS YALVAFRNDT W EGIEAGIK ...String:
MTWLPFIIII PLLGAFSMPI VSLLKGKAKE IWASMISFAT LIVGIQVFRE VWSKGTIVYT LGAPNPFGKA TFPIRIVWEV DKFGALMVL IVTFVSFLAV IYSIEYMKHD TGLEKFYTLI LILELGMLGI AITGDIFNFY VFLEIMSIAS YALVAFRNDT W EGIEAGIK YMFAGSLASS FVLLGIALLY GQYGTLTMGY LAVKIAENPT IVAKVALALF IGGLLFKSGA APVHMWLADA HP AAPSSIS AMLSGLVIKI GGIYAIARIV FSIFSPTINL GTIGWIIIIF ACITLIVGNA MAVVQEDLKR LLAYSSVGQI GYI LLGLGI GMVAYGTRVG EIALAGAIYH TVNHALMKAL LFLVAGAVIH EIGTRNMNEL SGLAKTMPKT TFAFLIGAAA IVGL PPLNG FASKWLIYES SALFNPILGA IAVIGTVFCT AAYVRALFTF FGRPSEKVTN ARDPGIAMML PMIILVVTII VMGFF PWQI SDRIMVPTAR ALWDVIDYIS SLMGGG

UniProtKB: Monovalent cation/H+ antiporter subunit D

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Macromolecule #2: Monovalent cation/H+ antiporter subunit C

MacromoleculeName: Monovalent cation/H+ antiporter subunit C / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 12.784348 KDa
Recombinant expressionOrganism: Pyrococcus furiosus (archaea)
SequenceString:
MIAFQYLTAT IMILLGIYAL LYKRNLIKLV LALNLIDSGI HLLLISEGYR MENGIPPTAP IYTGYEGGAM VAPIPQALVL TSIVIGVCV LSLAIALTVN AYRHYGTLDV TKLRRLRG

UniProtKB: Monovalent cation/H+ antiporter subunit C

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Macromolecule #3: MBH subunit

MacromoleculeName: MBH subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
Molecular weightTheoretical: 10.423586 KDa
Recombinant expressionOrganism: Pyrococcus furiosus (archaea)
SequenceString:
MHISKKKGVR KMNLDMIIQF IVLGGIILSS VLMIVTRDLL VAVLASAAMS LLLSLEFYML HAPDVAIAEA AVGAGVVTAL VMYAISKTE RWEREAP

UniProtKB: DUF4040 domain-containing protein

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Macromolecule #4: MBH subunit

MacromoleculeName: MBH subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 13.055353 KDa
Recombinant expressionOrganism: Pyrococcus furiosus (archaea)
SequenceString:
MFGYWDPLYF IIVFIIGLIL AYLLNLWAKK SGMGTREVGE GTKIFISGED PEKVIPGFEH LEGYYTGRNT MWGLVNGVKK FFATLKNDH TGLLPDYVSY LLMTTAFILV ILLLRG

UniProtKB: Uncharacterized protein

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Macromolecule #5: Mbh13 NADH dehydrogenase subunit

MacromoleculeName: Mbh13 NADH dehydrogenase subunit / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 35.414543 KDa
Recombinant expressionOrganism: Pyrococcus furiosus (archaea)
SequenceString: MKIVYGVIGL ILIYIYVSVV SLLFSGIDRK LVARMQRRIG PPILQPFYDF LKLMSKETII PKTANFMFKA APILMLATVI ALLAYTPLG FPPIFGTKGD IIVFIYLLTL ADFFLVVGVM SSGSPYGRIG AARGIALLVS REPAMMLGVF AVMWAISKLG V EKPFSLSS ...String:
MKIVYGVIGL ILIYIYVSVV SLLFSGIDRK LVARMQRRIG PPILQPFYDF LKLMSKETII PKTANFMFKA APILMLATVI ALLAYTPLG FPPIFGTKGD IIVFIYLLTL ADFFLVVGVM SSGSPYGRIG AARGIALLVS REPAMMLGVF AVMWAISKLG V EKPFSLSS LYEHTIWDFG PVAWVAGVVL IYVFMAWLAS EIEVGFFNIP EAEQEIAEGT LVEYSGRYLG IIKLAESIKE FI AASLVVA VLFPWQLNIP GVQGYLINLL LHTLKVFIVL LVSKTIFRTI TGRLKISQAV NLLWTRVFTA SVIGALLLAL GVM L

UniProtKB: Mbh13 NADH dehydrogenase subunit

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Macromolecule #6: Monovalent cation/H+ antiporter subunit B

MacromoleculeName: Monovalent cation/H+ antiporter subunit B / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 15.531277 KDa
Recombinant expressionOrganism: Pyrococcus furiosus (archaea)
SequenceString:
MNEDMGVIVR TNARALIPFI GIFGAYIVTH GHLTPGGGFQ GGATIAGAGV LFLIAFGVKA AKEKINKNLY SALEGLGGLV FLGAAMLGL SVAFFYNILW HEGPIFNSSP GTLLSAGFLP IMNLGVGLKV FTGLVSALFA LSVFRRWKS

UniProtKB: Monovalent cation/H+ antiporter subunit B

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Macromolecule #7: Monovalent cation/H+ antiporter subunit E

MacromoleculeName: Monovalent cation/H+ antiporter subunit E / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 18.750781 KDa
Recombinant expressionOrganism: Pyrococcus furiosus (archaea)
SequenceString:
MSFITAFIWA YFLWLVLTAG SKGMLWSTQE LIAGLIFASI VGYSTRNIIG EKASRFLNPV KWILFVAYAP VLFWGMVKAN LDVAYRVIT GKIRPGIVRV PVELENDAQY TILSNSITLT PGTLTVEACP EEKALYVHWI NIPEGLEWPE NSEPVSGPFE K WARRLGA

UniProtKB: Monovalent cation/H+ antiporter subunit E

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Macromolecule #8: MBH subunit

MacromoleculeName: MBH subunit / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 11.14966 KDa
Recombinant expressionOrganism: Pyrococcus furiosus (archaea)
SequenceString:
MKRALGFLSL LVIFASLLVA LSPEYGIKFG VGGEDWLKYR YTDNYYIEHG IEEVGGTNIV TDIVFDYRGY DTLGEATVLF TAIAGAVAL LRPWRREENE

UniProtKB: Uncharacterized protein

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Macromolecule #9: Monovalent cation/H+ antiporter subunit G

MacromoleculeName: Monovalent cation/H+ antiporter subunit G / type: protein_or_peptide / ID