7au6

Cytochrome c oxidase structure in O-state

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome c oxidase subunit 1-beta

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cytochrome c oxidase subunit 2 × 1 （P08306） Cytochrome c oxidase subunit 3 × 1 （P06030） Cytochrome c oxidase subunit 4 × 1 （P77921） HEME-A × 2 COPPER (II) ION × 1 CALCIUM ION × 1 OXYGEN MOLECULE × 6 HYDROGEN PEROXIDE × 1 MANGANESE (II) ION × 1 DINUCLEAR COPPER ION × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COX1B_PARDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–558； UniProt 1–558

Cytochrome c oxidase subunit 2

OrganismNot specified

UniProt P08306

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cytochrome c oxidase subunit 1-beta × 1 （P98002） Cytochrome c oxidase subunit 3 × 1 （P06030） Cytochrome c oxidase subunit 4 × 1 （P77921） HEME-A × 2 COPPER (II) ION × 1 CALCIUM ION × 1 OXYGEN MOLECULE × 6 HYDROGEN PEROXIDE × 1 MANGANESE (II) ION × 1 DINUCLEAR COPPER ION × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COX2_PARDE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–298； UniProt 1–298

Cytochrome c oxidase subunit 3

OrganismNot specified

UniProt P06030

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cytochrome c oxidase subunit 1-beta × 1 （P98002） Cytochrome c oxidase subunit 2 × 1 （P08306） Cytochrome c oxidase subunit 4 × 1 （P77921） HEME-A × 2 COPPER (II) ION × 1 CALCIUM ION × 1 OXYGEN MOLECULE × 6 HYDROGEN PEROXIDE × 1 MANGANESE (II) ION × 1 DINUCLEAR COPPER ION × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COX3_PARDE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–274； UniProt 1–274

Cytochrome c oxidase subunit 4

OrganismNot specified

UniProt P77921

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cytochrome c oxidase subunit 1-beta × 1 （P98002） Cytochrome c oxidase subunit 2 × 1 （P08306） Cytochrome c oxidase subunit 3 × 1 （P06030） HEME-A × 2 COPPER (II) ION × 1 CALCIUM ION × 1 OXYGEN MOLECULE × 6 HYDROGEN PEROXIDE × 1 MANGANESE (II) ION × 1 DINUCLEAR COPPER ION × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COX4_PARDE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–50； UniProt 1–50

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7au6
Deposition date deposition_date	2020-11-02
Structure title title	Cytochrome c oxidase structure in O-state
Keywords keywords	Terminal oxidase Cytochrome c oxidase aa3 oxidase, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7au6__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7au6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7au6__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	31.25 Å
Rg (electron density)	30.14 Å
Total Rg	30.84 Å
Atom count	8876
Residues	1092
Excluded volume	161700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7au6__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Description description	Cytochrome c oxidase subunit 1-beta
Molecular weight formula_weight	62486.6 kDa
EC 编号 ec_number	7.1.1.9
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9024

MADAAVHGHGDHHDTRGFFTRWFMSTNHKDIGILYLFTAGIVGLISVCFTVYMRMELQHPGVQYMCLEGARLIADASAECTPNGHLWNVMITYHGVLMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRLNNLSYWMYVCGVALGVASLLAPGGNDQMGSGVGWVLYPPLSTTEAGYSMDLAIFAVHVSGASSILGAINIITTFLNMRAPGMTLFKVPLFAWSVFITAWLILLSLPVLAGAITMLLMDRNFGTQFFDPAGGGDPVLYQHILWFFGHPEVYIIILPGFGIISHVISTFAKKPIFGYLPMVLAMAAIGILGFVVWAHHMYTAGMSLTQQAYFMLATMTIAVPTGIKVFSWIATMWGGSIEFKTPMLWAFGFLFLFTVGGVTGVVLSQAPLDRVYHDTYYVVAHFHYVMSLGAVFGIFAGVYYWIGKMSGRQYPEWAGQLHFWMMFIGSNLIFFPQHFLGRQGMPRRYIDYPVEFAYWNNISSIGAYISFASFLFFIGIVFYTLFAGKRVNVPNYWNEHADTLEWTLPSPPPEHTFETLPKREDWDRAHAH

Entity 2 Entity 2 polymer

Description description	Cytochrome c oxidase subunit 2
Molecular weight formula_weight	32563.6 kDa
EC 编号 ec_number	7.1.1.9
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MMAIATKRRGVAAVMSLGVATMTAVPALAQDVLGDLPVIGKPVNGGMNFQPASSPLAHDQQWLDHFVLYIITAVTIFVCLLLLICIVRFNRRANPVPARFTHNTPIEVIWTLVPVLILVAIGAFSLPILFRSQEMPNDPDLVIKAIGHQWYWSYEYPNDGVAFDALMLEKEALADAGYSEDEYLLATDNPVVVPVGKKVLVQVTATDVIHAWTIPAFAVKQDAVPGRIAQLWFSVDQEGVYFGQCSELCGINHAYMPIVVKAVSQEKYEAWLAGAKEEFAADASDYLPASPVKLASAE

Entity 3 Entity 3 polymer

Description description	Cytochrome c oxidase subunit 3
Molecular weight formula_weight	30808.2 kDa
EC 编号 ec_number	7.1.1.9
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MAHVKNHDYQILPPSIWPFFGAIGAFVMLTGAVAWMKGITFFGLPVEGPWMFLIGLVGVLYVMFGWWADVVNEGETGEHTPVVRIGLQYGFILFIMSEVMFFVAWFWAFIKNALYPMGPDSPIKDGVWPPEGIVTFDPWHLPLINTLILLLSGVAVTWAHHAFVLEGDRKTTINGLIVAVILGVCFTGLQAYEYSHAAFGLADTVYAGAFYMATGFHGAHVIIGTIFLFVCLIRLLKGQMTQKQHVGFEAAAWYWHFVDVVWLFLFVVIYIWGR

Entity 4 Entity 4 polymer

Description description	Cytochrome c oxidase subunit 4
Molecular weight formula_weight	5509.3 kDa
EC 编号 ec_number	7.1.1.9
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MASHHEITDHKHGEMDIRHQQATFAGFIKGATWVSILSIAVLVFLALANS

Entity 5 Entity 5 non-polymer

Description description	HEME-A
Molecular weight formula_weight	852.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	OXYGEN MOLECULE
Molecular weight formula_weight	32.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 9 Entity 9 non-polymer

Description description	HYDROGEN PEROXIDE
Molecular weight formula_weight	34.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	DINUCLEAR COPPER ION
Molecular weight formula_weight	127.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 non-polymer

Description description	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	790.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 13 Entity 13 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	148

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7au6A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	210 — Cytochrome C Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Cytochrome c oxidase-like, subunit I domain

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	321273

Cytochrome c oxidase structure in O-state

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome c oxidase subunit 1-beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome c oxidase subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome c oxidase subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome c oxidase subunit 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7au6__assembly_1__model_1

7au6__assembly_1__model_1 | I(q)

7au6__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)