8dh6

Cryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidase (Complex IV) extracted in lipid nanodiscs

Method: ELECTRON MICROSCOPY
▼

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

Cytochrome c oxidase subunit 1

OrganismNot specified

UniProt P00401

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 9 Cytochrome c oxidase subunit 2 × 1 (P00410) Cytochrome c oxidase subunit 3 × 1 (P00420) Cytochrome c oxidase subunit 4, mitochondrial × 1 (P04037) Cytochrome c oxidase subunit 5A, mitochondrial × 1 (P00424) Cytochrome c oxidase subunit 6, mitochondrial × 1 (P00427) Cytochrome c oxidase subunit 7, mitochondrial × 1 (P10174) Cytochrome c oxidase subunit 8, mitochondrial × 1 (P04039) Cytochrome c oxidase subunit 9, mitochondrial × 1 (P07255) CALCIUM ION × 1 MAGNESIUM ION × 1 COPPER (II) ION × 2 HEME-A × 2 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 10 ZINC ION × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name COX1_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain a; PDBConstruct 1–534; UniProt 1–534

Cytochrome c oxidase subunit 2

OrganismNot specified

UniProt P00410

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 9 Cytochrome c oxidase subunit 1 × 1 (P00401) Cytochrome c oxidase subunit 3 × 1 (P00420) Cytochrome c oxidase subunit 4, mitochondrial × 1 (P04037) Cytochrome c oxidase subunit 5A, mitochondrial × 1 (P00424) Cytochrome c oxidase subunit 6, mitochondrial × 1 (P00427) Cytochrome c oxidase subunit 7, mitochondrial × 1 (P10174) Cytochrome c oxidase subunit 8, mitochondrial × 1 (P04039) Cytochrome c oxidase subunit 9, mitochondrial × 1 (P07255) CALCIUM ION × 1 MAGNESIUM ION × 1 COPPER (II) ION × 2 HEME-A × 2 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 10 ZINC ION × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name COX2_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain b; PDBConstruct 1–236; UniProt 16–251

Cytochrome c oxidase subunit 3

OrganismNot specified

UniProt P00420

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 9 Cytochrome c oxidase subunit 1 × 1 (P00401) Cytochrome c oxidase subunit 2 × 1 (P00410) Cytochrome c oxidase subunit 4, mitochondrial × 1 (P04037) Cytochrome c oxidase subunit 5A, mitochondrial × 1 (P00424) Cytochrome c oxidase subunit 6, mitochondrial × 1 (P00427) Cytochrome c oxidase subunit 7, mitochondrial × 1 (P10174) Cytochrome c oxidase subunit 8, mitochondrial × 1 (P04039) Cytochrome c oxidase subunit 9, mitochondrial × 1 (P07255) CALCIUM ION × 1 MAGNESIUM ION × 1 COPPER (II) ION × 2 HEME-A × 2 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 10 ZINC ION × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name COX3_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain c; PDBConstruct 1–269; UniProt 1–269

Cytochrome c oxidase subunit 4, mitochondrial

OrganismNot specified

UniProt P04037

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 9 Cytochrome c oxidase subunit 1 × 1 (P00401) Cytochrome c oxidase subunit 2 × 1 (P00410) Cytochrome c oxidase subunit 3 × 1 (P00420) Cytochrome c oxidase subunit 5A, mitochondrial × 1 (P00424) Cytochrome c oxidase subunit 6, mitochondrial × 1 (P00427) Cytochrome c oxidase subunit 7, mitochondrial × 1 (P10174) Cytochrome c oxidase subunit 8, mitochondrial × 1 (P04039) Cytochrome c oxidase subunit 9, mitochondrial × 1 (P07255) CALCIUM ION × 1 MAGNESIUM ION × 1 COPPER (II) ION × 2 HEME-A × 2 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 10 ZINC ION × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name COX4_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain d; PDBConstruct 1–130; UniProt 26–155

Cytochrome c oxidase subunit 5A, mitochondrial

OrganismNot specified

UniProt P00424

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 9 Cytochrome c oxidase subunit 1 × 1 (P00401) Cytochrome c oxidase subunit 2 × 1 (P00410) Cytochrome c oxidase subunit 3 × 1 (P00420) Cytochrome c oxidase subunit 4, mitochondrial × 1 (P04037) Cytochrome c oxidase subunit 6, mitochondrial × 1 (P00427) Cytochrome c oxidase subunit 7, mitochondrial × 1 (P10174) Cytochrome c oxidase subunit 8, mitochondrial × 1 (P04039) Cytochrome c oxidase subunit 9, mitochondrial × 1 (P07255) CALCIUM ION × 1 MAGNESIUM ION × 1 COPPER (II) ION × 2 HEME-A × 2 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 10 ZINC ION × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name COX5A_YEAST
Isoform —
PDB entities 5
Chains and sequence ranges Author chain e; PDBConstruct 1–133; UniProt 21–153

Cytochrome c oxidase subunit 6, mitochondrial

OrganismNot specified

UniProt P00427

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 9 Cytochrome c oxidase subunit 1 × 1 (P00401) Cytochrome c oxidase subunit 2 × 1 (P00410) Cytochrome c oxidase subunit 3 × 1 (P00420) Cytochrome c oxidase subunit 4, mitochondrial × 1 (P04037) Cytochrome c oxidase subunit 5A, mitochondrial × 1 (P00424) Cytochrome c oxidase subunit 7, mitochondrial × 1 (P10174) Cytochrome c oxidase subunit 8, mitochondrial × 1 (P04039) Cytochrome c oxidase subunit 9, mitochondrial × 1 (P07255) CALCIUM ION × 1 MAGNESIUM ION × 1 COPPER (II) ION × 2 HEME-A × 2 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 10 ZINC ION × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name COX6_YEAST
Isoform —
PDB entities 6
Chains and sequence ranges Author chain f; PDBConstruct 1–108; UniProt 41–148

Cytochrome c oxidase subunit 7, mitochondrial

OrganismNot specified

UniProt P10174

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 9 Cytochrome c oxidase subunit 1 × 1 (P00401) Cytochrome c oxidase subunit 2 × 1 (P00410) Cytochrome c oxidase subunit 3 × 1 (P00420) Cytochrome c oxidase subunit 4, mitochondrial × 1 (P04037) Cytochrome c oxidase subunit 5A, mitochondrial × 1 (P00424) Cytochrome c oxidase subunit 6, mitochondrial × 1 (P00427) Cytochrome c oxidase subunit 8, mitochondrial × 1 (P04039) Cytochrome c oxidase subunit 9, mitochondrial × 1 (P07255) CALCIUM ION × 1 MAGNESIUM ION × 1 COPPER (II) ION × 2 HEME-A × 2 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 10 ZINC ION × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name COX7_YEAST
Isoform —
PDB entities 7
Chains and sequence ranges Author chain g; PDBConstruct 1–59; UniProt 2–60

Cytochrome c oxidase subunit 8, mitochondrial

OrganismNot specified

UniProt P04039

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 9 Cytochrome c oxidase subunit 1 × 1 (P00401) Cytochrome c oxidase subunit 2 × 1 (P00410) Cytochrome c oxidase subunit 3 × 1 (P00420) Cytochrome c oxidase subunit 4, mitochondrial × 1 (P04037) Cytochrome c oxidase subunit 5A, mitochondrial × 1 (P00424) Cytochrome c oxidase subunit 6, mitochondrial × 1 (P00427) Cytochrome c oxidase subunit 7, mitochondrial × 1 (P10174) Cytochrome c oxidase subunit 9, mitochondrial × 1 (P07255) CALCIUM ION × 1 MAGNESIUM ION × 1 COPPER (II) ION × 2 HEME-A × 2 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 10 ZINC ION × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name COX8_YEAST
Isoform —
PDB entities 8
Chains and sequence ranges Author chain h; PDBConstruct 1–51; UniProt 28–78

Cytochrome c oxidase subunit 9, mitochondrial

OrganismNot specified

UniProt P07255

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 9 Cytochrome c oxidase subunit 1 × 1 (P00401) Cytochrome c oxidase subunit 2 × 1 (P00410) Cytochrome c oxidase subunit 3 × 1 (P00420) Cytochrome c oxidase subunit 4, mitochondrial × 1 (P04037) Cytochrome c oxidase subunit 5A, mitochondrial × 1 (P00424) Cytochrome c oxidase subunit 6, mitochondrial × 1 (P00427) Cytochrome c oxidase subunit 7, mitochondrial × 1 (P10174) Cytochrome c oxidase subunit 8, mitochondrial × 1 (P04039) CALCIUM ION × 1 MAGNESIUM ION × 1 COPPER (II) ION × 2 HEME-A × 2 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 10 ZINC ION × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name COX9_YEAST
Isoform —
PDB entities 9
Chains and sequence ranges Author chain i; PDBConstruct 1–55; UniProt 2–56

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id8dh6
Deposition date deposition_date2022-06-25
Structure title titleCryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidase (Complex IV) extracted in lipid nanodiscs
Keywords keywordscytochrome c oxidase, Complex IV, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
▼

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.

8dh6__assembly_1__model_1

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

Download this curve (.dat)

8dh6__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

8dh6__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)37.63 Å
Rg (electron density)36.36 Å
Total Rg36.89 Å
Atom count12901
Residues1560
Excluded volume235590 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 8dh6__assembly_1__model_1 nonameric (9) Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (15)

▼

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id8dh6a01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology210 — Cytochrome C Oxidase; Chain A
Homologous superfamily homologous superfamily10 — Cytochrome c oxidase-like, subunit I domain
Domain ID domain_id8dh6b01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily90 —
Domain ID domain_id8dh6b02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
▶

7. Citations (1)