5weh

Cytochrome c oxidase from Rhodobacter sphaeroides in the reduced state

Method: X-RAY DIFFRACTION

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

Cytochrome c oxidase subunit 1

Rhodobacter sphaeroides

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 （Q03736） Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3) × 1 （P84153） Aa3-type cytochrome c oxidase subunit IV × 1 （Q8KRK5） HEME-A × 2 COPPER (I) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 DODECYL-ALPHA-D-MALTOSIDE × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Cytochrome c oxidase subunit 2 × 1 （Q03736） Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3) × 1 （P84153） Aa3-type cytochrome c oxidase subunit IV × 1 （Q8KRK5） HEME-A × 2 COPPER (I) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 DODECYL-ALPHA-D-MALTOSIDE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COX1_RHOSH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–566； UniProt 1–566 Author chain G； PDBConstruct 1–566； UniProt 1–566

Cytochrome c oxidase subunit 2

Rhodobacter sphaeroides

UniProt Q03736

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 × 1 （P33517） Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3) × 1 （P84153） Aa3-type cytochrome c oxidase subunit IV × 1 （Q8KRK5） HEME-A × 2 COPPER (I) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 DODECYL-ALPHA-D-MALTOSIDE × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Cytochrome c oxidase subunit 1 × 1 （P33517） Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3) × 1 （P84153） Aa3-type cytochrome c oxidase subunit IV × 1 （Q8KRK5） HEME-A × 2 COPPER (I) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 DODECYL-ALPHA-D-MALTOSIDE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COX2_RHOSH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–256； UniProt 26–281 Author chain H； PDBConstruct 1–256； UniProt 26–281

Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3)

Rhodobacter sphaeroides

UniProt P84153

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 × 1 （P33517） Cytochrome c oxidase subunit 2 × 1 （Q03736） Aa3-type cytochrome c oxidase subunit IV × 1 （Q8KRK5） HEME-A × 2 COPPER (I) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 DODECYL-ALPHA-D-MALTOSIDE × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Cytochrome c oxidase subunit 1 × 1 （P33517） Cytochrome c oxidase subunit 2 × 1 （Q03736） Aa3-type cytochrome c oxidase subunit IV × 1 （Q8KRK5） HEME-A × 2 COPPER (I) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 DODECYL-ALPHA-D-MALTOSIDE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P84153_RHOSH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–266； UniProt 1–266 Author chain I； PDBConstruct 1–266； UniProt 1–266

Aa3-type cytochrome c oxidase subunit IV

Rhodobacter sphaeroides

UniProt Q8KRK5

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 × 1 （P33517） Cytochrome c oxidase subunit 2 × 1 （Q03736） Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3) × 1 （P84153） HEME-A × 2 COPPER (I) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 DODECYL-ALPHA-D-MALTOSIDE × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Cytochrome c oxidase subunit 1 × 1 （P33517） Cytochrome c oxidase subunit 2 × 1 （Q03736） Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3) × 1 （P84153） HEME-A × 2 COPPER (I) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 DODECYL-ALPHA-D-MALTOSIDE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8KRK5_RHOSH
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–50； UniProt 12–61 Author chain J； PDBConstruct 1–50； UniProt 12–61

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	5weh
Deposition date deposition_date	2017-07-10
Structure title title	Cytochrome c oxidase from Rhodobacter sphaeroides in the reduced state
Keywords keywords	oxidase, Complex IV, reduced, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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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.

5weh__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5weh__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5weh__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	31.36 Å
Rg (electron density)	30.01 Å
Total Rg	30.72 Å
Atom count	8989
Residues	1106
Excluded volume	163310 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5weh__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5weh__assembly_2__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 (11)

Entity 1 Entity 1 polymer

Description description	Cytochrome c oxidase subunit 1
Molecular weight formula_weight	63195.4 kDa
EC 编号 ec_number	1.9.3.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,G
Atom count atom_count	17909

MADAAIHGHEHDRRGFFTRWFMSTNHKDIGVLYLFTGGLVGLISVAFTVYMRMELMAPGVQFMCAEHLESGLVKGFFQSLWPSAVENCTPNGHLWNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAVASLFAPGGNGQLGSGIGWVLYPPLSTSESGYSTDLAIFAVHLSGASSILGAINMITTFLNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDPVLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWAHHMYTAGLSLTQQSYFMMATMVIAVPTGIKIFSWIATMWGGSIELKTPMLWALGFLFLFTVGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWAGKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPEAFATWNFVSSLGAFLSFASFLFFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHTFEQLPKREDWERAPAH

Source Source

Source organism organism	Rhodobacter sphaeroides
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	Rhodobacter sphaeroides

Entity 2 Entity 2 polymer

Description description	Cytochrome c oxidase subunit 2
Molecular weight formula_weight	29365.4 kDa
EC 编号 ec_number	1.9.3.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,H

QQQSLEIIGRPQPGGTGFQPSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAWTIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSPATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAFGVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQHHHHHH

Source Source

Source organism organism	Rhodobacter sphaeroides
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	Rhodobacter sphaeroides

Entity 3 Entity 3 polymer

Description description	Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3)
Molecular weight formula_weight	30197.2 kDa
EC 编号 ec_number	1.9.3.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,I

MAHAKNHDYHILPPSIWPFMASVGAFVMLFGAVLWMHGSGPWMGLIGLVVVLYTMFGWWSDVVTESLEGDHTPVVRLGLRWGFILFIMSEVMFFSAWFWSFFKHALYPMGPESPIIDGIFPPEGIITFDPWHLPLINTLILLCSGCAATWAHHALVHENNRRDVAWGLALAIALGALFTVFQAYEYSHAAFGFAGNIYGANFFMATGFHGFHVIVGTIFLLVCLIRVQRGHFTPEKHVGFEAAIWYWHFVDVVWLFLFASIYIWGQ

Source Source

Source organism organism	Rhodobacter sphaeroides
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	Rhodobacter sphaeroides

Entity 4 Entity 4 polymer

Description description	Aa3-type cytochrome c oxidase subunit IV
Molecular weight formula_weight	5278.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,J

ADHSHPAHGHVAGSMDITQQEKTFAGFVRMVTWAAVVIVAALIFLALANA

Source Source

Source organism organism	Rhodobacter sphaeroides
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	Rhodobacter sphaeroides

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	4

Entity 6 Entity 6 non-polymer

Description description	COPPER (I) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	1,2-Distearoyl-sn-glycerophosphoethanolamine
Molecular weight formula_weight	748.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 10 Entity 10 non-polymer

Description description	DODECYL-ALPHA-D-MALTOSIDE
Molecular weight formula_weight	510.6 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	5wehA00
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

Domain ID domain_id	5wehB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	5wehB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5wehC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	5wehC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	80 — Cytochrome c oxidase, subunit III, four-helix bundle

Domain ID domain_id	5wehD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	160 — Bacterial aa3 type cytochrome c oxidase subunit IV

Domain ID domain_id	5wehG00
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

Domain ID domain_id	5wehH01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	5wehH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5wehI01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	5wehI02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	80 — Cytochrome c oxidase, subunit III, four-helix bundle

Domain ID domain_id	5wehJ00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	160 — Bacterial aa3 type cytochrome c oxidase subunit IV

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Unit-cell length a length_a	339.221 Å
Unit-cell length b length_b	339.221 Å
Unit-cell length c length_c	89.199 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	3.450 Å
Low-resolution limit resolution_low	28.450 Å
R factor r_factor	0.2244
R_work r_work	0.2232
R_free r_free	0.2615

Cytochrome c oxidase from Rhodobacter sphaeroides in the reduced state

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

Cytochrome c oxidase subunit 1

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 polypeptide III (Cytochrome AA3 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

Aa3-type cytochrome c oxidase subunit IV

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

5weh__assembly_2__model_1

5weh__assembly_2__model_1 | I(q)

5weh__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

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 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)