6xkw

R. capsulatus CIII2CIV bipartite super-complex (SC-2A) with CcoH/cy

Method: ELECTRON MICROSCOPY

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

Cytochrome c oxidase, Cbb3-type, subunit I

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Cytochrome c oxidase, Cbb3-type, subunit II × 1 （D5ARP5） Cbb3-type cytochrome c oxidase subunit CcoP × 1 （D5ARP7） Cytochrome c oxidase, Cbb3-type, biogenesis protein CcoH × 1 （D5ARP9） Cytochrome c-type cyt cy × 1 （Q05389） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （D5ANZ2） Cytochrome b × 2 （D5ANZ3） Cytochrome c1 × 2 （D5ANZ4） HEME C × 11 COPPER (II) ION × 1 FE2/S2 (INORGANIC) CLUSTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D5ARP4_RHOCB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain n； PDBConstruct 1–532； UniProt 1–532

Cytochrome c oxidase, Cbb3-type, subunit II

OrganismNot specified

UniProt D5ARP5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Cytochrome c oxidase, Cbb3-type, subunit I × 1 （D5ARP4） Cbb3-type cytochrome c oxidase subunit CcoP × 1 （D5ARP7） Cytochrome c oxidase, Cbb3-type, biogenesis protein CcoH × 1 （D5ARP9） Cytochrome c-type cyt cy × 1 （Q05389） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （D5ANZ2） Cytochrome b × 2 （D5ANZ3） Cytochrome c1 × 2 （D5ANZ4） HEME C × 11 COPPER (II) ION × 1 FE2/S2 (INORGANIC) CLUSTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D5ARP5_RHOCB
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain o； PDBConstruct 1–242； UniProt 1–242

Cbb3-type cytochrome c oxidase subunit CcoP

Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)

UniProt D5ARP7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Cytochrome c oxidase, Cbb3-type, subunit I × 1 （D5ARP4） Cytochrome c oxidase, Cbb3-type, subunit II × 1 （D5ARP5） Cytochrome c oxidase, Cbb3-type, biogenesis protein CcoH × 1 （D5ARP9） Cytochrome c-type cyt cy × 1 （Q05389） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （D5ANZ2） Cytochrome b × 2 （D5ANZ3） Cytochrome c1 × 2 （D5ANZ4） HEME C × 11 COPPER (II) ION × 1 FE2/S2 (INORGANIC) CLUSTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCOP_RHOCB
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain p； PDBConstruct 1–297； UniProt 1–297

Cytochrome c oxidase, Cbb3-type, biogenesis protein CcoH

OrganismNot specified

UniProt D5ARP9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Cytochrome c oxidase, Cbb3-type, subunit I × 1 （D5ARP4） Cytochrome c oxidase, Cbb3-type, subunit II × 1 （D5ARP5） Cbb3-type cytochrome c oxidase subunit CcoP × 1 （D5ARP7） Cytochrome c-type cyt cy × 1 （Q05389） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （D5ANZ2） Cytochrome b × 2 （D5ANZ3） Cytochrome c1 × 2 （D5ANZ4） HEME C × 11 COPPER (II) ION × 1 FE2/S2 (INORGANIC) CLUSTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D5ARP9_RHOCB
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain h； PDBConstruct 1–151； UniProt 1–151

Cytochrome c-type cyt cy

OrganismNot specified

UniProt Q05389

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Cytochrome c oxidase, Cbb3-type, subunit I × 1 （D5ARP4） Cytochrome c oxidase, Cbb3-type, subunit II × 1 （D5ARP5） Cbb3-type cytochrome c oxidase subunit CcoP × 1 （D5ARP7） Cytochrome c oxidase, Cbb3-type, biogenesis protein CcoH × 1 （D5ARP9） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （D5ANZ2） Cytochrome b × 2 （D5ANZ3） Cytochrome c1 × 2 （D5ANZ4） HEME C × 11 COPPER (II) ION × 1 FE2/S2 (INORGANIC) CLUSTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYCY_RHOCB
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain Y； PDBConstruct 1–199； UniProt 1–199

Ubiquinol-cytochrome c reductase iron-sulfur subunit

Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)

UniProt D5ANZ2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Cytochrome c oxidase, Cbb3-type, subunit I × 1 （D5ARP4） Cytochrome c oxidase, Cbb3-type, subunit II × 1 （D5ARP5） Cbb3-type cytochrome c oxidase subunit CcoP × 1 （D5ARP7） Cytochrome c oxidase, Cbb3-type, biogenesis protein CcoH × 1 （D5ARP9） Cytochrome c-type cyt cy × 1 （Q05389） Cytochrome b × 2 （D5ANZ3） Cytochrome c1 × 2 （D5ANZ4） HEME C × 11 COPPER (II) ION × 1 FE2/S2 (INORGANIC) CLUSTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UCRI_RHOCB
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain E； PDBConstruct 1–191； UniProt 1–191 Author chain R； PDBConstruct 1–191； UniProt 1–191

Cytochrome b

Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)

UniProt D5ANZ3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Cytochrome c oxidase, Cbb3-type, subunit I × 1 （D5ARP4） Cytochrome c oxidase, Cbb3-type, subunit II × 1 （D5ARP5） Cbb3-type cytochrome c oxidase subunit CcoP × 1 （D5ARP7） Cytochrome c oxidase, Cbb3-type, biogenesis protein CcoH × 1 （D5ARP9） Cytochrome c-type cyt cy × 1 （Q05389） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （D5ANZ2） Cytochrome c1 × 2 （D5ANZ4） HEME C × 11 COPPER (II) ION × 1 FE2/S2 (INORGANIC) CLUSTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYB_RHOCB
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain C； PDBConstruct 1–437； UniProt 1–437 Author chain P； PDBConstruct 1–437； UniProt 1–437

Cytochrome c1

Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)

UniProt D5ANZ4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Cytochrome c oxidase, Cbb3-type, subunit I × 1 （D5ARP4） Cytochrome c oxidase, Cbb3-type, subunit II × 1 （D5ARP5） Cbb3-type cytochrome c oxidase subunit CcoP × 1 （D5ARP7） Cytochrome c oxidase, Cbb3-type, biogenesis protein CcoH × 1 （D5ARP9） Cytochrome c-type cyt cy × 1 （Q05389） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （D5ANZ2） Cytochrome b × 2 （D5ANZ3） HEME C × 11 COPPER (II) ION × 1 FE2/S2 (INORGANIC) CLUSTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CY1_RHOCB
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain D； PDBConstruct 1–279； UniProt 1–279 Author chain Q； PDBConstruct 1–279； UniProt 1–279

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	6xkw
Deposition date deposition_date	2020-06-27
Structure title title	R. capsulatus CIII2CIV bipartite super-complex (SC-2A) with CcoH/cy
Keywords keywords	cytochrome bc1, cbb3-COX, Complex III, Complex IV, OXIDOREDUCTASE, TRANSLOCASE-Oxidoreductase complex; TRANSLOCASE/Oxidoreductase
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.

6xkw__assembly_1__model_1

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

Download this curve (.dat)

6xkw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6xkw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	50.48 Å
Rg (electron density)	50.11 Å
Total Rg	50.15 Å
Atom count	20831
Residues	2648
Excluded volume	374440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6xkw__assembly_1__model_1`	undecameric （11）	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, Cbb3-type, subunit I
Molecular weight formula_weight	58975.1 kDa
EC 编号 ec_number	1.9.3.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	n
Atom count atom_count	20831

MWDYVKLVALGVVVAIAAYAASQARDLPYMVNMVEVALAAVIAFIWVLRTMGDAKPSKDEYFDGVIRAGVIATTFWGIVGFLVAVIIAFQLAFPALNLEFGNGMLNFGRLRPLHTSAVIFAFGGNALIASAFYVVQRTSAARLFGGTALGWFVFWGWQLIIVTAATSYLLGGSQGKEYAELNWHLDILVAIVWVAYLIAFLGTIFKRKEPHIYVANWFYLSFIVTIAMLHIVNNLAVPVSIFGTKSVQLMAGVQDAMTQWWYGHNAVGFFLTAGFLGMMYYFVPKQAERPVYSYKLSIVHFWALIFLYIWAGPHHLHYTALPDWASTLGMVMSVILWMPSWGGMINGLMTLSGAWDKLRTDPVIRMMVVSIGFYGMSTFEGPMMSIKAVNSLSHYTDWTIGHVHSGALGWNGMITFGMLYFLTPRLWGRSGLYSLKLVSWHFWLATIGIVLYASSMWVSGIMEGLMWREVDAQGFLVNGFADTVGAKFPMNVVRGVGGVLYLTGGLIMAYNLWATVAKQPKTANLAVAVPAE

Entity 2 Entity 2 polymer

Description description	Cytochrome c oxidase, Cbb3-type, subunit II
Molecular weight formula_weight	26998.7 kDa
EC 编号 ec_number	1.9.3.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	o

MSIMDKHHVLEKNATLLLIFAFLVVTIGGIVEIAPLFYLENTIEKVEGMRPYTPLELTGRDIYIREGCYVCHSQMIRPMRDEVERYGHYSLAAESMYDHPFQWGSKRTGPDLARVGGRYSDAWHVEHLSNPQSVVPESVMPSYSYLANVPLDSTWIEDRVSTDALVGVPYSAEMIAAAKADFVAQADPNADSATLVANYGEKVNIRNFDGKPGLTEMDALVAYLQVLGTMVDFSTFQPVASR

Entity 3 Entity 3 polymer

Description description	Cbb3-type cytochrome c oxidase subunit CcoP
Molecular weight formula_weight	31739.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	p

MSKKPTTKKEVQTTGHSWDGIEELNTPLPRWWLWTFYATIVWGVAYSIAMPAWPIFASGATPGILGSSTRADVEKDIAKFAEMNKAVEDKLVATDLTAIAADPELVTYTRNAGAAVFRTWCAQCHGAGAGGNTGFPSLLDGDWLHGGSIETIYTNIKHGIRDPLDPDTLPVANMPAHLTDELLEPAQIDDVVQYVLKISGQPADEARATAGQQVFADNCVSCHGEDAKGMVEMGAPNLTDGIWLYGGDANTITTTIQLGRGGVMPSWSWAADGAKPRLSEAQIRAVASYVHSLGGGQ

Source Source

Source organism organism	Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)
NCBI taxonomy ID ncbi_taxonomy_id	272942
Host organism host_organism	Rhodobacter capsulatus SB 1003

Entity 4 Entity 4 polymer

Description description	Cytochrome c oxidase, Cbb3-type, biogenesis protein CcoH
Molecular weight formula_weight	16285.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	h

MAKPLTGRKVLLMFVAFFGLIIAVNVTMAVQAVKTFPGLEVANSYVASQTFDADRAAQERLGWTVKPAYADGVLSLDIRDRAGQPAPLGQLEVLVGRTTMAAEDRTPQMTRTDGVYSAPLSLAPGAWLIHLSATSADGVLFRQRLDFFVEG

Entity 5 Entity 5 polymer

Description description	Cytochrome c-type cyt cy
Molecular weight formula_weight	20681.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

MLVKTHITKIGVTLFAVALFYGFIYMLSNSLFATRPATAVAVGADGKALLPSVDEAAMPAKAPAAAAPAAETAEAAAPAEPAAPPPPAYVEVDPATITGDAKAGEEKFNKTCKACHKIDGKNAVGPHLNGVIGRATATVEGFKYSTAMKNHVGNWTPERLDIYLVSPKAEVPGTKMSFVGLPEAADRANVIAYLNTLPR

Entity 6 Entity 6 polymer

Description description	Ubiquinol-cytochrome c reductase iron-sulfur subunit
Molecular weight formula_weight	20465.1 kDa
EC 编号 ec_number	7.1.1.8
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,R

MSHAEDNAGTRRDFLYHATAATGVVVTGAAVWPLINQMNASADVKAMASIFVDVSAVEVGTQLTVKWRGKPVFIRRRDEKDIELARSVPLGALRDTSAENANKPGAEATDENRTLPAFDGTNTGEWLVMLGVCTHLGCVPMGDKSGDFGGWFCPCHGSHYDSAGRIRKGPAPRNLDIPVAAFVDETTIKLG

Source Source

Source organism organism	Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)
NCBI taxonomy ID ncbi_taxonomy_id	272942
Host organism host_organism	Rhodobacter capsulatus SB 1003

Entity 7 Entity 7 polymer

Description description	Cytochrome b
Molecular weight formula_weight	49386.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSGIPHDHYEPKTGIEKWLHDRLPIVGLVYDTIMIPTPKNLNWWWIWGIVLAFTLVLQIVTGIVLAMHYTPHVDLAFASVEHIMRDVNGGWAMRYIHANGASLFFLAVYIHIFRGLYYGSYKAPREITWIVGMVIYLLMMGTAFMGYVLPWGQMSFWGATVITGLFGAIPGIGPSIQAWLLGGPAVDNATLNRFFSLHYLLPFVIAALVAIHIWAFHTTGNNNPTGVEVRRTSKADAEKDTLPFWPYFVIKDLFALALVLLGFFAVVAYMPNYLGHPDNYVQANPLSTPAHIVPEWYFLPFYAILRAFAADVWVVILVDGLTFGIVDAKFFGVIAMFGAIAVMALAPWLDTSKVRSGAYRPKFRMWFWFLVLDFVVLTWVGAMPTEYPYDWISLIASTYWFAYFLVILPLLGATEKPEPIPASIEEDFNSHYGNPAE

Source Source

Source organism organism	Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)
NCBI taxonomy ID ncbi_taxonomy_id	272942
Host organism host_organism	Rhodobacter capsulatus SB 1003

Entity 8 Entity 8 polymer

Description description	Cytochrome c1
Molecular weight formula_weight	30352.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MKKLLISAVSALVLGSGAAFANSNVPDHAFSFEGIFGKYDQAQLRRGFQVYNEVCSACHGMKFVPIRTLADDGGPQLDPTFVREYAAGLDTIIDKDSGEERDRKETDMFPTRVGDGMGPDLSVMAKARAGFSGPAGSGMNQLFKGMGGPEYIYNYVIGFEENPECAPEGIDGYYYNKTFQIGGVPDTCKDAAGVKITHGSWARMPPPLVDDQVTYEDGTPATVDQMAQDVSAFLMWAAEPKLVARKQMGLVAMVMLGLLSVMLYLTNKRLWAPYKGHKA

Source Source

Source organism organism	Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)
NCBI taxonomy ID ncbi_taxonomy_id	272942
Host organism host_organism	Rhodobacter capsulatus SB 1003

Entity 9 Entity 9 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 10 Entity 10 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 11 Entity 11 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	2

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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	5.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	14978

R. capsulatus CIII2CIV bipartite super-complex (SC-2A) with CcoH/cy

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

Cytochrome c oxidase, Cbb3-type, subunit I

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, Cbb3-type, subunit II

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cbb3-type cytochrome c oxidase subunit CcoP

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, Cbb3-type, biogenesis protein CcoH

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-type cyt cy

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquinol-cytochrome c reductase iron-sulfur subunit

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 b

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 c1

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

6xkw__assembly_1__model_1

6xkw__assembly_1__model_1 | I(q)

6xkw__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 (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer