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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 / electron transport
Function / homologyCytochrome c oxidase, subunit II / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome C oxidase subunit II, transmembrane domain / NADH-ubiquinone reductase complex 1 MLRQ subunit / Cupredoxin / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb ...Cytochrome c oxidase, subunit II / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome C oxidase subunit II, transmembrane domain / NADH-ubiquinone reductase complex 1 MLRQ subunit / Cupredoxin / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome c oxidase, subunit Vb / Copper centre Cu(A) / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase subunit I / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase, subunit Vb, zinc binding site / Cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase subunit III-like superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase subunit III / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit I, copper-binding site / Cytochrome c oxidase subunit III-like / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / Heme-copper oxidase subunit III family profile. / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase chain VIIB / Cytochrome oxidase subunit I profile. / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome c oxidase subunit VIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase subunit VIIc / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome oxidase c subunit VIb / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VIa / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / TP53 Regulates Metabolic Genes / Cytochrome c oxidase subunit Vb / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c oxidase subunit III / Cytochrome C oxidase subunit II, periplasmic domain / Respiratory electron transport / NADH-ubiquinone reductase complex 1 MLRQ subunit / positive regulation of hydrogen peroxide biosynthetic process / positive regulation of necrotic cell death / mitochondrial respiratory chain complex I / mitochondrial electron transport, NADH to ubiquinone / oxidoreduction-driven active transmembrane transporter activity / mitochondrial respirasome assembly / respiratory chain complex IV assembly / respiratory chain complex IV / NADH dehydrogenase (ubiquinone) activity / mitochondrial respiratory chain complex III / regulation of oxidative phosphorylation / proton transmembrane transport / mitochondrial respirasome / ATP synthesis coupled electron transport / electron transport coupled proton transport / mitochondrial ATP synthesis coupled proton transport / mitochondrial respiratory chain complex IV / positive regulation of ATP biosynthetic process / cytochrome-c oxidase / respiratory gaseous exchange / cytochrome-c oxidase activity / mitochondrial electron transport, cytochrome c to oxygen / enzyme regulator activity / response to copper ion / aerobic respiration / cerebellum development / substantia nigra development / central nervous system development / response to electrical stimulus / generation of precursor metabolites and energy
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsGu, J. / Zong, S. / Wu, M. / Yang, M.
Funding supportChina , 5 items
OrganizationGrant numberCountry
National Basic Research Program of China(973 Program)2017YFA0504600China
National Basic Research Program of China(973 Program)2016YFA0501100China
National Science Foundation (China)31625008China
National Natural Science Foundation of China21532004China
National Natural Science Foundation of China31570733China
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 22, 2018 / Release: Feb 27, 2019

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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)216,23525
Polyers210,53814
Non-polymers5,69711
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)65930
ΔGint (kcal/M)-589
Surface area (Å2)71290

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Components

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

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


Mass: 57076.914 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P00395, cytochrome-c oxidase
#2: Protein/peptide Cytochrome c oxidase subunit 2 / / Cytochrome c oxidase polypeptide II


Mass: 25580.900 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P00403
#3: Protein/peptide Cytochrome c oxidase subunit 3 / / Cytochrome c oxidase polypeptide III


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


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


Mass: 10627.033 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P10606
#7: Protein/peptide 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: (natural) Homo sapiens (human) / References: UniProt: P12074
#8: Protein/peptide 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: (natural) Homo sapiens (human) / References: UniProt: P14854
#9: Protein/peptide Cytochrome c oxidase subunit 6C / / Cytochrome c oxidase polypeptide VIc


Mass: 8596.200 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P09669
#10: Protein/peptide 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: (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: (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: (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: (natural) Homo sapiens (human) / References: UniProt: P10176
#14: Protein/peptide Cytochrome c oxidase subunit NDUFA4 /


Mass: 9137.486 Da / Num. of mol.: 1 / 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 / Formula: Cu / Copper
#16: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#17: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Formula: C49H56FeN4O6 / Heme A
#18: Chemical ChemComp-PEE / 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 749.073 Da / Num. of mol.: 3 / Formula: C41H83NO8P / Discrete optimized protein energy / 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 / Formula: C81H156O17P2 / Cardiolipin / Comment: phospholipid *YM
#20: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human cytochrome c oxidase / Type: COMPLEX / Details: 14 subunits / Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14 / 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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
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 / Number of particles: 1010000 / Symmetry type: POINT

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