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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


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 / 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
Similarity search - Domain/homology
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 ...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 (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-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing 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
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  • 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
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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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 280 pix.
= 304.64 Å		1.09 Å/pix.
x 280 pix.
= 304.64 Å		1.09 Å/pix.
x 280 pix.
= 304.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.088 Å
Density

Histogram

Histogram (log scale)
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: MrpA C-terminal/MbhD 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: Hydrogenase

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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: MrpA C-terminal/MbhE domain-containing 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: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 13.521957 KDa
Recombinant expressionOrganism: Pyrococcus furiosus (archaea)
SequenceString:
MIAYYLIIAF LGISVTFNML GSIALHRFPD VYTRLHGATK CTTFGTIFAA LAVITHAIVK LQATGNPKYL QMAIHSFVAM LALLLTNPV GAHAIAKAAH KTGYLPKRAV VDAYLEKERG EKNES

UniProtKB: Monovalent cation/H+ antiporter subunit G

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Macromolecule #10: Monovalent cation/H+ antiporter subunit F

MacromoleculeName: Monovalent cation/H+ antiporter subunit F / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 9.063924 KDa
Recombinant expressionOrganism: Pyrococcus furiosus (archaea)
SequenceString:
MIFFYATLLI GIAGIITFIR LALGPTVPDR VVAVDTLNTL IVAIMLLLGA AYERAIYIDI AIVYALLSYV GTLVIAKYLQ GGLQ

UniProtKB: Monovalent cation/H+ antiporter subunit F

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Macromolecule #11: Probable membrane-bound hydrogenase subunit mbhJ

MacromoleculeName: Probable membrane-bound hydrogenase subunit mbhJ / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO / EC number: ferredoxin hydrogenase
Source (natural)Organism: Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
Molecular weightTheoretical: 18.324152 KDa
Recombinant expressionOrganism: Pyrococcus furiosus (archaea)
SequenceString:
MTNNSERKRL EKRIAQLCKF IGRSPWVFHV NSGSCNGCDI EIIAALTPRY DAERFGVKLV GSPRHADILL VTGPVTNQSL ERVKLVYEQ TPDPKIVIAI GACPTGGSVF YESPFTNAPL DRIIPVDVFV PGCPPRPEAI LHGVVLALEK LAKMIKGEVP P EEGEENE

UniProtKB: Probable membrane-bound hydrogenase subunit mbhJ

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Macromolecule #12: Membrane-bound hydrogenase subunit beta

MacromoleculeName: Membrane-bound hydrogenase subunit beta / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO / EC number: ferredoxin hydrogenase
Source (natural)Organism: Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
Molecular weightTheoretical: 20.213092 KDa
Recombinant expressionOrganism: Pyrococcus furiosus (archaea)
SequenceString:
MSKAEMVANK IKERFPNAEV VVKTNKWGRE RVWVRISREE YKELMKFIRE LDPEAHYSIG IEQDWGDELG FLNHILLFYD EPPGVSLLI DVHAPKDNPV LPDTSDIFPI SLQFEREGME MVGLDFEGAP DKRRLFLPDD FPEGIYPLRT DEKGVPEEMV K NAGHPYLL RREKK

UniProtKB: Membrane-bound hydrogenase subunit beta

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Macromolecule #13: Membrane-bound hydrogenase subunit alpha

MacromoleculeName: Membrane-bound hydrogenase subunit alpha / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO / EC number: ferredoxin hydrogenase
Source (natural)Organism: Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
Molecular weightTheoretical: 43.008723 KDa
Recombinant expressionOrganism: Pyrococcus furiosus (archaea)
SequenceString: MKKVEYWVKI PFGPIHPGLE EPEKFIITLD GERIVNVDVK LGYNLRGVQW IGMRRNYVQI MYLAERMCGI CSFSHNHTYV RAVEEMAGI EVPERAEYIR VIVGELERIH SHLLNLGVVG HDIGYDTVLH LTWLARERVM DVLEAVSGNR VNYSMVTIGG V RRDIGEKQ ...String:
MKKVEYWVKI PFGPIHPGLE EPEKFIITLD GERIVNVDVK LGYNLRGVQW IGMRRNYVQI MYLAERMCGI CSFSHNHTYV RAVEEMAGI EVPERAEYIR VIVGELERIH SHLLNLGVVG HDIGYDTVLH LTWLARERVM DVLEAVSGNR VNYSMVTIGG V RRDIGEKQ KRLILDMIKY YREVLPQIED VFLHDSTIEA RLRDVAVVPK KLAIEMGAVG PTARGSGIKE DSRWSEQLGV YP DLGIKPV TPEDVTGEKA RGDVYDRMAV RIGELWMSLD LLEHALDQMP EGKIKTFPKD NILVAKLKLL GDGEGIGRYE APR GELVHY VRGQKGRDGP VRWKPREPTF PNLFTIAKAL EGNELADLVV AIASIDPCLS CTDR

UniProtKB: Membrane-bound hydrogenase subunit alpha

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Macromolecule #14: NADH-plastoquinone oxidoreductase subunit

MacromoleculeName: NADH-plastoquinone oxidoreductase subunit / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 15.707697 KDa
Recombinant expressionOrganism: Pyrococcus furiosus (archaea)
SequenceString:
MIRLPLLPTV IKNLFKKPAT NPFPKTEPVP VPEDFRGKLV YNVDKCVGCR MCVTVCPAGV FVYLPEIRKV TLWIGRCVMC KQCVDVCPT AALQMSDEFL LASYDKYDAK LIYLTPEEAE DIKKKLEEAN KAKAEKQASK

UniProtKB: NADH-plastoquinone oxidoreductase subunit

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Macromolecule #15: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 15 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #16: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)

MacromoleculeName: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / type: ligand / ID: 16 / Number of copies: 1 / Formula: NFU
Molecular weightTheoretical: 195.591 Da
Chemical component information

ChemComp-NFU:
formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 131679
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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  • 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

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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

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