1zrt

Rhodobacter capsulatus cytochrome bc1 complex with stigmatellin bound

Method: X-RAY DIFFRACTION

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

Cytochrome b

Rhodobacter capsulatus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Cytochrome c1 × 2 （D5ANZ4） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （D5ANZ2） PROTOPORPHYRIN IX CONTAINING FE × 4 STIGMATELLIN A × 2 UNKNOWN LIGAND × 4 HEME C × 2 FE2/S2 (INORGANIC) CLUSTER × 2 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE × 1	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	1
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

UniProt D5ANZ4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Cytochrome b × 2 （D5ANZ3） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （D5ANZ2） PROTOPORPHYRIN IX CONTAINING FE × 4 STIGMATELLIN A × 2 UNKNOWN LIGAND × 4 HEME C × 2 FE2/S2 (INORGANIC) CLUSTER × 2 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE × 1	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	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–258； UniProt 22–279 Author chain Q； PDBConstruct 1–258； UniProt 22–279

Ubiquinol-cytochrome c reductase iron-sulfur subunit

Rhodobacter capsulatus

UniProt D5ANZ2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Cytochrome b × 2 （D5ANZ3） Cytochrome c1 × 2 （D5ANZ4） PROTOPORPHYRIN IX CONTAINING FE × 4 STIGMATELLIN A × 2 UNKNOWN LIGAND × 4 HEME C × 2 FE2/S2 (INORGANIC) CLUSTER × 2 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE × 1	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	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–191； UniProt 1–191 Author chain R； PDBConstruct 1–191； UniProt 1–191

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	1zrt
Deposition date deposition_date	2005-05-22
Structure title title	Rhodobacter capsulatus cytochrome bc1 complex with stigmatellin bound
Keywords keywords	;CYTOCHROME BC1, MEMBRANE PROTEIN, HEME PROTEIN, RIESKE IRON SULFUR PROTEIN, CYTOCHROME B, CYTOCHROME C1, COMPLEX III, OXIDOREDUCTASE, REDOX ENZYME, RESPIRATORY CHAIN, STIGMATELLIN, ELECTRON TRANSPORT ;; ELECTRON TRANSPORT
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.

1zrt__assembly_1__model_1

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

Download this curve (.dat)

1zrt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zrt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.71 Å
Rg (electron density)	37.48 Å
Total Rg	37.93 Å
Atom count	13901
Residues	1724
Excluded volume	250040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zrt__assembly_1__model_1`	hexameric （6）	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 (9)

Entity 1 Entity 1 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
Atom count atom_count	13919

MSGIPHDHYEPKTGIEKWLHDRLPIVGLVYDTIMIPTPKNLNWWWIWGIVLAFTLVLQIVTGIVLAMHYTPHVDLAFASVEHIMRDVNGGWAMRYIHANGASLFFLAVYIHIFRGLYYGSYKAPREITWIVGMVIYLLMMGTAFMGYVLPWGQMSFWGATVITGLFGAIPGIGPSIQAWLLGGPAVDNATLNRFFSLHYLLPFVIAALVAIHIWAFHTTGNNNPTGVEVRRTSKADAEKDTLPFWPYFVIKDLFALALVLLGFFAVVAYMPNYLGHPDNYVQANPLSTPAHIVPEWYFLPFYAILRAFAADVWVVILVDGLTFGIVDAKFFGVIAMFGAIAVMALAPWLDTSKVRSGAYRPKFRMWFWFLVLDFVVLTWVGAMPTEYPYDWISLIASTYWFAYFLVILPLLGATEKPEPIPASIEEDFNSHYGNPAE

Source Source

Source organism organism	Rhodobacter capsulatus
NCBI taxonomy ID ncbi_taxonomy_id	1061
Host organism host_organism	Rhodobacter capsulatus

Entity 2 Entity 2 polymer

Description description	Cytochrome c1
Molecular weight formula_weight	28321.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

NSNVPDHAFSFEGIFGKYDQAQLRRGFQVYNEVCSACHGMKFVPIRTLADDGGPQLDPTFVREYAAGLDTIIDKDSGEERDRKETDMFPTRVGDGMGPDLSVMAKARAGFSGPAGSGMNQLFKGMGGPEYIYNYVIGFEENPECAPEGIDGYYYNKTFQIGGVPDTCKDAAGVKITHGSWARMPPPLVDDQVTYEDGTPATVDQMAQDVSAFLMWAAEPKLVARKQMGLVAMVMLGLLSVMLYLTNKRLWAPYKGHKA

Source Source

Source organism organism	Rhodobacter capsulatus
NCBI taxonomy ID ncbi_taxonomy_id	1061
Host organism host_organism	Rhodobacter capsulatus

Entity 3 Entity 3 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
NCBI taxonomy ID ncbi_taxonomy_id	1061
Host organism host_organism	Rhodobacter capsulatus

Entity 4 Entity 4 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	man
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	STIGMATELLIN A
Molecular weight formula_weight	514.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	UNKNOWN LIGAND
Molecular weight formula_weight	103.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 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

Entity 9 Entity 9 non-polymer

Description description	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
Molecular weight formula_weight	266.3 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	1zrtC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	810 — Cytochrome Bc1 Complex; Chain C
Homologous superfamily homologous superfamily	10 — Cytochrome Bc1 Complex; Chain C

Domain ID domain_id	1zrtE01
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	510 — Single helix bin

Domain ID domain_id	1zrtE02
Class class	2 — Mainly Beta
Architecture architecture	102 — 3-layer Sandwich
Topology topology	10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily	10 — Rieske [2Fe-2S] iron-sulphur domain

Domain ID domain_id	1zrtP00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	810 — Cytochrome Bc1 Complex; Chain C
Homologous superfamily homologous superfamily	10 — Cytochrome Bc1 Complex; Chain C

Domain ID domain_id	1zrtR01
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	510 — Single helix bin

Domain ID domain_id	1zrtR02
Class class	2 — Mainly Beta
Architecture architecture	102 — 3-layer Sandwich
Topology topology	10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily	10 — Rieske [2Fe-2S] iron-sulphur domain

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Unit-cell length a length_a	95.633 Å
Unit-cell length b length_b	154.360 Å
Unit-cell length c length_c	103.057 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.57 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.510 Å
Low-resolution limit resolution_low	59.770 Å
R factor r_factor	0.2240
R_work r_work	0.2207
R_free r_free	0.2887

Rhodobacter capsulatus cytochrome bc1 complex with stigmatellin bound

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

Cytochrome b

State in the Current Structure

Other States of the Same Protein in the Database

Cytochrome c1

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquinol-cytochrome c reductase iron-sulfur subunit

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1zrt__assembly_1__model_1

1zrt__assembly_1__model_1 | I(q)

1zrt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (9)

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 non-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

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Rhodobacter capsulatus cytochrome bc1 complex with stigmatellin bound

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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1zrt__assembly_1__model_1

1zrt__assembly_1__model_1 | I(q)

1zrt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (9)

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 non-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

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)