2OCC | pdb_00002occ

BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDIZED STATE

PDB DOI: https://doi.org/10.2210/pdb2OCC/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bos taurus
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 1998-05-26 Released: 1999-01-13
Deposition Author(s): Tsukihara, T., Yao, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.244 (Depositor)
R-Value Work:
0.209 (Depositor)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase.

Yoshikawa, S., Shinzawa-Itoh, K., Nakashima, R., Yaono, R., Yamashita, E., Inoue, N., Yao, M., Fei, M.J., Libeu, C.P., Mizushima, T., Yamaguchi, H., Tomizaki, T., Tsukihara, T.

(1998) Science 280: 1723-1729

PubMed: 9624044 Search on PubMed
DOI: https://doi.org/10.1126/science.280.5370.1723
Primary Citation Related Structures:
1OCO, 1OCR, 1OCZ, 2OCC

PubMed Abstract:
Crystal structures of bovine heart cytochrome c oxidase in the fully oxidized, fully reduced, azide-bound, and carbon monoxide-bound states were determined at 2.30, 2.35, 2.9, and 2.8 angstrom resolution, respectively. An aspartate residue apart from the O2 reduction site exchanges its effective accessibility to the matrix aqueous phase for one to the cytosolic phase concomitantly with a significant decrease in the pK of its carboxyl group, on reduction of the metal sites. The movement indicates the aspartate as the proton pumping site. A tyrosine acidified by a covalently linked imidazole nitrogen is a possible proton donor for the O2 reduction by the enzyme.

Organizational Affiliation

Department of Life Science, Himeji Institute of Technology and CREST, Japan Science and Technology Corporation (JST), Kamigohri Akoh, Hyogo 678-1297, Japan.

Macromolecule Content

Total Structure Weight: 413.72 kDa
Atom Count: 28,864
Modeled Residue Count: 3,564
Deposited Residue Count: 3,612
Unique protein chains: 13

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C OXIDASE	A, N	514	Bos taurus	Mutation(s): 0 EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P00396 (Bos taurus) Explore P00396 Go to UniProtKB: P00396
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00396
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C OXIDASE	B, O	227	Bos taurus	Mutation(s): 0 EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P68530 (Bos taurus) Explore P68530 Go to UniProtKB: P68530
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68530
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C OXIDASE	C, P	261	Bos taurus	Mutation(s): 0 EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P00415 (Bos taurus) Explore P00415 Go to UniProtKB: P00415
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00415
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C OXIDASE	D, Q	147	Bos taurus	Mutation(s): 0 EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for P00423 (Bos taurus) Explore P00423 Go to UniProtKB: P00423
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00423
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C OXIDASE	E, R	109	Bos taurus	Mutation(s): 0 EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for P00426 (Bos taurus) Explore P00426 Go to UniProtKB: P00426
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00426
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C OXIDASE	F, S	98	Bos taurus	Mutation(s): 0 EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for P00428 (Bos taurus) Explore P00428 Go to UniProtKB: P00428
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00428
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C OXIDASE	G, T	84	Bos taurus	Mutation(s): 0 EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for P07471 (Bos taurus) Explore P07471 Go to UniProtKB: P07471
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07471
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C OXIDASE	H, U	85	Bos taurus	Mutation(s): 0 EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for P00429 (Bos taurus) Explore P00429 Go to UniProtKB: P00429
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00429
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C OXIDASE	I, V	73	Bos taurus	Mutation(s): 0 EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for P04038 (Bos taurus) Explore P04038 Go to UniProtKB: P04038
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04038
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C OXIDASE	J, W	59	Bos taurus	Mutation(s): 0 EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for P07470 (Bos taurus) Explore P07470 Go to UniProtKB: P07470
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07470
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C OXIDASE	K, X	56	Bos taurus	Mutation(s): 0 EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for P13183 (Bos taurus) Explore P13183 Go to UniProtKB: P13183
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13183
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C OXIDASE	L, Y	47	Bos taurus	Mutation(s): 0 EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for P00430 (Bos taurus) Explore P00430 Go to UniProtKB: P00430
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00430
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C OXIDASE	M, Z	46	Bos taurus	Mutation(s): 0 EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for P10175 (Bos taurus) Explore P10175 Go to UniProtKB: P10175
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10175
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEA Query on HEA Download:Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain NA [auth N] SDF format, chain MA [auth N] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain NA [auth N] MOL2 format, chain MA [auth N] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain NA [auth N] mmCIF format, chain MA [auth N]	DA [auth A], EA [auth A], MA [auth N], NA [auth N]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain DA [auth A] Focus chain EA [auth A] Focus chain MA [auth N] Focus chain NA [auth N]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain IA [auth F] SDF format, chain RA [auth S] MOL2 format, chain IA [auth F] MOL2 format, chain RA [auth S] mmCIF format, chain IA [auth F] mmCIF format, chain RA [auth S]	IA [auth F], RA [auth S]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain IA [auth F] Focus chain RA [auth S]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain JA [auth N] SDF format, chain PA [auth O] SDF format, chain QA [auth O] MOL2 format, chain AA [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain JA [auth N] MOL2 format, chain PA [auth O] MOL2 format, chain QA [auth O] mmCIF format, chain AA [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain JA [auth N] mmCIF format, chain PA [auth O] mmCIF format, chain QA [auth O]	AA [auth A] GA [auth B] HA [auth B] JA [auth N] PA [auth O] AA [auth A], GA [auth B], HA [auth B], JA [auth N], PA [auth O], QA [auth O]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain JA [auth N] Focus chain PA [auth O] Focus chain QA [auth O]
PER Query on PER Download:Ideal Coordinates CCD File SDF format, chain FA [auth A] SDF format, chain OA [auth N] MOL2 format, chain FA [auth A] MOL2 format, chain OA [auth N] mmCIF format, chain FA [auth A] mmCIF format, chain OA [auth N]	FA [auth A], OA [auth N]	PEROXIDE ION O₂ ANAIPYUSIMHBEL-UHFFFAOYSA-N		Interactions Focus chain FA [auth A] Focus chain OA [auth N]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain KA [auth N] MOL2 format, chain BA [auth A] MOL2 format, chain KA [auth N] mmCIF format, chain BA [auth A] mmCIF format, chain KA [auth N]	BA [auth A], KA [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain KA [auth N]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain LA [auth N] MOL2 format, chain CA [auth A] MOL2 format, chain LA [auth N] mmCIF format, chain CA [auth A] mmCIF format, chain LA [auth N]	CA [auth A], LA [auth N]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain LA [auth N]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.244 (Depositor)
R-Value Work: 0.209 (Depositor)
R-Value Observed: 0.209 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 189.1	α = 90
b = 210.5	β = 90
c = 178.6	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
TSUKI	data reduction
X-PLOR	model building
X-PLOR	refinement
TSUKI	data scaling
X-PLOR	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 1999-01-13

Deposition Author(s):

Tsukihara, T.

Yao, M.

Revision History (Full details and data files)

Version 1.0: 1999-01-13
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2023-08-09
Changes: Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-30
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

2OCC | pdb_00002occ

BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDIZED STATE

Literature

Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)