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- PDB-5z62: Structure of human cytochrome c oxidase -

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Entry
Database: PDB / ID: 5z62
TitleStructure of human cytochrome c oxidase
Components(Cytochrome c oxidase subunit ...) x 14
KeywordsELECTRON TRANSPORT / cytochrome c oxidase
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 ...: / 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 / mitochondrial electron transport, NADH to ubiquinone / response to electrical stimulus / NADH dehydrogenase (ubiquinone) activity / 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 / generation of precursor metabolites and energy / respiratory electron transport chain / TP53 Regulates Metabolic Genes / 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 / protein-containing complex binding / mitochondrion / nucleoplasm / metal ion binding / membrane / cytosol
Similarity search - Function
NADH-ubiquinone reductase complex 1 MLRQ subunit / NADH-ubiquinone reductase complex 1 MLRQ subunit / Cytochrome C Oxidase; Chain F / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 ...NADH-ubiquinone reductase complex 1 MLRQ subunit / NADH-ubiquinone reductase complex 1 MLRQ subunit / Cytochrome C Oxidase; Chain F / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit VIIa / Cytochrome C Oxidase; Chain I / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome C Oxidase; Chain G / Cytochrome c oxidase, subunit VIa / Cytochrome C Oxidase; Chain M / Cytochrome C Oxidase; Chain L / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase, subunit Va/VI / Cytochrome C Oxidase; Chain J / Helix Hairpins - #90 / 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; Chain A / Cytochrome c oxidase-like, subunit I domain / 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 III domain / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / 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. / Cupredoxins - blue copper proteins / Cupredoxin / Few Secondary Structures / Irregular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Helix Hairpins / Alpha Horseshoe / Arc Repressor Mutant, subunit A / Up-down Bundle / Immunoglobulin-like / Sandwich
Similarity search - Domain/homology
CARDIOLIPIN / COPPER (II) ION / HEME-A / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Cytochrome c oxidase subunit NDUFA4 / 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 / Cytochrome c oxidase subunit NDUFA4 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGu, J. / Zong, S. / Wu, M. / Yang, M.
Funding support China, 5items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFA0504600 China
National Basic Research Program of China (973 Program)2016YFA0501100 China
National Science Foundation (China)31625008 China
National Natural Science Foundation of China21532004 China
National Natural Science Foundation of China31570733 China
CitationJournal: Cell Res / Year: 2018
Title: Structure of the intact 14-subunit human cytochrome c oxidase.
Authors: Shuai Zong / Meng Wu / Jinke Gu / Tianya Liu / Runyu Guo / Maojun Yang /
Abstract: Respiration is one of the most basic features of living organisms, and the electron transport chain complexes are probably the most complicated protein system in mitochondria. Complex-IV is the ...Respiration is one of the most basic features of living organisms, and the electron transport chain complexes are probably the most complicated protein system in mitochondria. Complex-IV is the terminal enzyme of the electron transport chain, existing either as randomly scattered complexes or as a component of supercomplexes. NDUFA4 was previously assumed as a subunit of complex-I, but recent biochemical data suggested it may be a subunit of complex-IV. However, no structural evidence supporting this notion was available till now. Here we obtained the 3.3 Å resolution structure of complex-IV derived from the human supercomplex IIIIIV and assigned the NDUFA4 subunit into complex-IV. Intriguingly, NDUFA4 lies exactly at the dimeric interface observed in previously reported crystal structures of complex-IV homodimer which would preclude complex-IV dimerization. Combining previous structural and biochemical data shown by us and other groups, we propose that the intact complex-IV is a monomer containing 14 subunits.
History
DepositionJan 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 2.0Apr 9, 2025Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_audit_support / pdbx_database_status / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_chiral / struct_conn / struct_conn_type
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

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Assembly

Deposited unit
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
N: Cytochrome c oxidase subunit NDUFA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,22025
Polymers210,53814
Non-polymers5,68211
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area65930 Å2
ΔGint-589 kcal/mol
Surface area71290 Å2

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Components

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Cytochrome c oxidase subunit ... , 14 types, 14 molecules ABCDEFGHIJKLMN

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


Mass: 57076.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00395, cytochrome-c oxidase
#2: 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
#3: Protein Cytochrome c oxidase subunit 3 / Cytochrome c oxidase polypeptide III


Mass: 29844.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00414
#4: 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: 16890.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P13073
#5: Protein Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase polypeptide Va


Mass: 12517.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P20674
#6: Protein Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase polypeptide Vb


Mass: 10627.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P10606
#7: Protein Cytochrome c oxidase subunit 6A1, mitochondrial / Cytochrome c oxidase polypeptide VIa-liver / Cytochrome c oxidase subunit VIA-liver / COX VIa-L


Mass: 8691.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P12074
#8: Protein Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit VIb isoform 1 / COX VIb-1


Mass: 9757.906 Da / Num. of mol.: 1 / Fragment: UNP residues 5-86 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14854
#9: Protein Cytochrome c oxidase subunit 6C / Cytochrome c oxidase polypeptide VIc


Mass: 8596.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09669
#10: Protein Cytochrome c oxidase subunit 7A2, mitochondrial / Cytochrome c oxidase subunit VIIa-liver/heart / Cytochrome c oxidase subunit VIIaL


Mass: 6196.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14406
#11: Protein/peptide Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase polypeptide VIIb


Mass: 5488.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P24311
#12: Protein/peptide Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase polypeptide VIIc


Mass: 5363.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15954
#13: Protein/peptide Cytochrome c oxidase subunit 8A, mitochondrial / Cytochrome c oxidase polypeptide VIII-liver/heart / Cytochrome c oxidase subunit 8-2


Mass: 4769.651 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P10176
#14: Protein Cytochrome c oxidase subunit NDUFA4


Mass: 9137.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00483

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Non-polymers , 6 types, 11 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-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#18: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#19: 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
#20: 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 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: human cytochrome c oxidase / Type: COMPLEX / Details: 14 subunits / Entity ID: #1-#14 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding 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: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.56 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1010000 / Symmetry type: POINT

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