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- PDB-9fks: Respiratory supercomplex CIII2-CIV2 from alphaproteobacterium -

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Basic information

Entry
Database: PDB / ID: 9fks
TitleRespiratory supercomplex CIII2-CIV2 from alphaproteobacterium
Components
  • (Cytochrome c oxidase subunit ...) x 2
  • Aa3 type cytochrome c oxidase subunit IV
  • Cytochrome b
  • Cytochrome c, class I
  • Cytochrome c1
  • Ubiquinol-cytochrome c reductase iron-sulfur subunit
  • cytochrome-c oxidase
KeywordsELECTRON TRANSPORT / Supercomplex / multi-subunit membrane protein complex / electron transport chain / native purification
Function / homology
Function and homology information


aerobic electron transport chain / respiratory chain complex IV / cytochrome-c oxidase / respiratory chain complex III / oxidative phosphorylation / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport ...aerobic electron transport chain / respiratory chain complex IV / cytochrome-c oxidase / respiratory chain complex III / oxidative phosphorylation / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / copper ion binding / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Cytochrome c oxidase, subunit IV, bacterial aa3 type / Bacterial aa3 type cytochrome c oxidase subunit IV superfamily / Bacterial aa3 type cytochrome c oxidase subunit IV / Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome c oxidase, subunit I bacterial type / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit II / Cytochrome c, class IA/ IB / Cytochrome c oxidase subunit I domain ...Cytochrome c oxidase, subunit IV, bacterial aa3 type / Bacterial aa3 type cytochrome c oxidase subunit IV superfamily / Bacterial aa3 type cytochrome c oxidase subunit IV / Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome c oxidase, subunit I bacterial type / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit II / Cytochrome c, class IA/ IB / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Cytochrome b / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c1 / Cytochrome c oxidase-like, subunit I domain / Cytochrome C1 family / Cytochrome oxidase subunit I profile. / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Rieske iron-sulphur protein, C-terminal / Cytochrome c / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / Chem-DU0 / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE ...1,2-Distearoyl-sn-glycerophosphoethanolamine / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / Chem-DU0 / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / : / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / UBIQUINONE-10 / Aa3 type cytochrome c oxidase subunit IV / Cytochrome c, class I / Cytochrome c oxidase subunit 1 / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cytochrome b / Cytochrome c1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesParacoccus denitrificans PD1222 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.31 Å
AuthorsYaikhomba, M. / Hirst, J. / Croll, T.I. / Spikes, T.E. / Agip, A.N.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 and MC_UU_00028/1 United Kingdom
CitationJournal: To Be Published
Title: Minimal supercomplexes in alphaproteobacteria reveal conserved structural mechanisms for efficient respiration
Authors: Yaikhomba, M. / Hirst, J. / Croll, T.I. / Spikes, T.E.
History
DepositionJun 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: Cytochrome b
b: Cytochrome c1
c: Ubiquinol-cytochrome c reductase iron-sulfur subunit
d: Cytochrome b
e: Cytochrome c1
f: Ubiquinol-cytochrome c reductase iron-sulfur subunit
g: Cytochrome c oxidase subunit 1
h: Cytochrome c oxidase subunit 2
i: cytochrome-c oxidase
j: Aa3 type cytochrome c oxidase subunit IV
k: Cytochrome c oxidase subunit 1
l: Cytochrome c oxidase subunit 2
m: cytochrome-c oxidase
n: Aa3 type cytochrome c oxidase subunit IV
o: Cytochrome c, class I
p: Cytochrome c, class I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)583,82891
Polymers538,72116
Non-polymers45,10675
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 6 types, 12 molecules adbecfimjnop

#1: Protein Cytochrome b


Mass: 50154.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B4F3
#2: Protein Cytochrome c1


Mass: 46904.332 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B4F4
#3: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 20889.236 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B4F2, quinol-cytochrome-c reductase
#6: Protein cytochrome-c oxidase / Cytochrome aa3 subunit 3 / Cytochrome c oxidase polypeptide III


Mass: 30833.162 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1BA37, cytochrome-c oxidase
#7: Protein Aa3 type cytochrome c oxidase subunit IV


Mass: 7351.497 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1AZ52
#8: Protein Cytochrome c, class I


Mass: 18177.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B311

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Cytochrome c oxidase subunit ... , 2 types, 4 molecules gkhl

#4: Protein Cytochrome c oxidase subunit 1


Mass: 62486.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B3D7, cytochrome-c oxidase
#5: Protein Cytochrome c oxidase subunit 2


Mass: 32563.643 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1BA41, cytochrome-c oxidase

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Non-polymers , 15 types, 75 molecules

#9: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#10: Chemical
ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#13: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#15: Chemical
ChemComp-DU0 / 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol


Mass: 516.752 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C32H52O5
#16: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#17: Chemical
ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C39H77O8P / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#19: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#21: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#22: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2
#23: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1Respiratory supercomplex CIII2-CIV2 from alphaproteobacteriumCOMPLEX#1-#80NATURAL
2Alphaproteobacterial respiratory complex III (ubiquinone-cytochrome c oxidoreductase, cytochrome bc1)COMPLEX#1-#31NATURAL
3Alphaproteobacterial respiratory complex IV (Cytochrome c oxidase, aa3-type)COMPLEX#4-#71NATURAL
4Transmembrane-anchored cytochrome c (c552)COMPLEX#81NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Paracoccus denitrificans PD1222 (bacteria)318586
22Paracoccus denitrificans PD1222 (bacteria)318586
33Paracoccus denitrificans PD1222 (bacteria)318586
44Paracoccus denitrificans PD1222 (bacteria)318586
Buffer solutionpH: 7.5
SpecimenConc.: 2.5 mg/ml / Embedding 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 / Nominal defocus max: 2700 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 55.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10322 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 120.15 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006535938
ELECTRON MICROSCOPYf_angle_d1.090548843
ELECTRON MICROSCOPYf_chiral_restr0.05515043
ELECTRON MICROSCOPYf_plane_restr0.00935811
ELECTRON MICROSCOPYf_dihedral_angle_d15.577212934

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