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- PDB-9i6f: Cryo-EM structure of HIGD2A bound complex IV -

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Basic information

Entry
Database: PDB / ID: 9i6f
TitleCryo-EM structure of HIGD2A bound complex IV
Components
  • (Cytochrome c oxidase subunit ...) x 13
  • HIG1 domain family member 2A, mitochondrial
KeywordsMEMBRANE PROTEIN / Human mitochondria / respirasome complex / assembly / cytochrome c oxidase / complex IV / HIGD2A
Function / homology
Function and homology information


Complex IV assembly / respiratory chain complex IV assembly / Respiratory electron transport / mitochondrial respirasome assembly / respiratory gaseous exchange by respiratory system / cellular respiration / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / mitochondrial electron transport, cytochrome c to oxygen ...Complex IV assembly / respiratory chain complex IV assembly / Respiratory electron transport / mitochondrial respirasome assembly / respiratory gaseous exchange by respiratory system / cellular respiration / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / response to copper ion / response to electrical stimulus / ATP synthesis coupled electron transport / enzyme regulator activity / lactation / response to nutrient / substantia nigra development / Mitochondrial protein degradation / aerobic respiration / cerebellum development / central nervous system development / TP53 Regulates Metabolic Genes / respiratory electron transport chain / generation of precursor metabolites and energy / Cytoprotection by HMOX1 / mitochondrial intermembrane space / mitochondrial membrane / response to oxidative stress / response to hypoxia / oxidoreductase activity / electron transfer activity / mitochondrial inner membrane / mitochondrial matrix / copper ion binding / heme binding / negative regulation of apoptotic process / mitochondrion / nucleoplasm / metal ion binding / membrane / cytosol
Similarity search - Function
: / Hypoxia induced protein, domain / Hypoxia induced protein conserved region / HIG1 domain profile. / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII ...: / Hypoxia induced protein, domain / Hypoxia induced protein conserved region / HIG1 domain profile. / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome C oxidase chain VIIB / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit Vb superfamily / 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 / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cupredoxin
Similarity search - Domain/homology
CARDIOLIPIN / COPPER (II) ION / HEME-A / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PGV / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 8A, mitochondrial ...CARDIOLIPIN / COPPER (II) ION / HEME-A / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PGV / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 8A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6A1, mitochondrial / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 7A2, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial / HIG1 domain family member 2A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsNguyen, M.D. / Rorbach, J. / Singh, V.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: To Be Published
Title: Structural basis for late maturation steps of mitochondrial respiratory chain complex IV within the human respirasome
Authors: Nguyen, M.D. / Singh, V. / Rorbach, J.
History
DepositionJan 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 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
N: HIG1 domain family member 2A, mitochondrial
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase subunit 3
D: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
E: Cytochrome c oxidase subunit 5A, mitochondrial
F: Cytochrome c oxidase subunit 5B, mitochondrial
G: Cytochrome c oxidase subunit 6A1, mitochondrial
H: Cytochrome c oxidase subunit 6B1
I: Cytochrome c oxidase subunit 6C
J: Cytochrome c oxidase subunit 7A2, mitochondrial
K: Cytochrome c oxidase subunit 7B, mitochondrial
L: Cytochrome c oxidase subunit 7C, mitochondrial
M: Cytochrome c oxidase subunit 8A, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,12227
Polymers238,94614
Non-polymers7,17513
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 , 1 types, 1 molecules N

#1: Protein HIG1 domain family member 2A, mitochondrial / RCF1 homolog B / RCF1b


Mass: 11542.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BW72

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Cytochrome c oxidase subunit ... , 13 types, 13 molecules ABCDEFGHIJKLM

#2: Protein Cytochrome c oxidase subunit 1 / Cytochrome c oxidase polypeptide I


Mass: 57104.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00395, cytochrome-c oxidase
#3: Protein Cytochrome c oxidase subunit 2 / Cytochrome c oxidase polypeptide II


Mass: 25580.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00403, cytochrome-c oxidase
#4: Protein Cytochrome c oxidase subunit 3 / Cytochrome c oxidase polypeptide III


Mass: 30003.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00414, cytochrome-c oxidase
#5: Protein Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase polypeptide IV / Cytochrome c oxidase subunit IV isoform 1 / COX IV-1


Mass: 19609.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P13073
#6: Protein Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase polypeptide Va


Mass: 16785.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P20674
#7: Protein Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase polypeptide Vb


Mass: 13714.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P10606
#8: Protein Cytochrome c oxidase subunit 6A1, mitochondrial / Cytochrome c oxidase polypeptide VIa-liver / Cytochrome c oxidase subunit VIA-liver / COX VIa-L


Mass: 12173.858 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P12074
#9: Protein Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit VIb isoform 1 / COX VIb-1


Mass: 10204.382 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14854
#10: Protein Cytochrome c oxidase subunit 6C / Cytochrome c oxidase polypeptide VIc


Mass: 8798.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09669
#11: Protein Cytochrome c oxidase subunit 7A2, mitochondrial / Cytochrome c oxidase subunit VIIa-liver/heart / Cytochrome c oxidase subunit VIIa-L / Cytochrome c ...Cytochrome c oxidase subunit VIIa-liver/heart / Cytochrome c oxidase subunit VIIa-L / Cytochrome c oxidase subunit VIIaL


Mass: 9409.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14406
#12: Protein Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase polypeptide VIIb


Mass: 9172.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P24311
#13: Protein Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase polypeptide VIIc


Mass: 7256.501 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15954
#14: Protein Cytochrome c oxidase subunit 8A, mitochondrial / Cytochrome c oxidase polypeptide VIII-liver/heart / Cytochrome c oxidase subunit 8-2


Mass: 7589.089 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P10176

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Non-polymers , 7 types, 13 molecules

#15: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#16: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#17: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#18: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#20: 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
#21: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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

ComponentName: Complex IV / Type: CELL / Entity ID: #1-#14 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Details: 25 mM HEPES-KOH pH=7.5, 50 mM KCl, 20 mM Mg(OAc)2, 0.01% (v/v) LMNG, 0.001 % cardiolipin, 0.001 % GD, 0.1mM DTT
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMpotassium chlorideKCl1
225 mMHepesC8H18N2O4S1
320 mMMagnesium acetateMg(CH3COO)21
40.01 %LMNGC47H88O221
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 17476

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Processing

EM softwareName: PHENIX / Version: 1.21rc1_5156 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129242 / Symmetry type: POINT
Atomic model buildingPDB-ID: 5Z62

5z62


Accession code: 5Z62 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.95 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00215617
ELECTRON MICROSCOPYf_angle_d0.82521185
ELECTRON MICROSCOPYf_dihedral_angle_d7.7042342
ELECTRON MICROSCOPYf_chiral_restr0.0362258
ELECTRON MICROSCOPYf_plane_restr0.0042598

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