2qjp

Crystal structure of wild type rhodobacter sphaeroides with stigmatellin and antimycin inhibited

Method: X-RAY DIFFRACTION

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

Cytochrome b

Rhodobacter sphaeroides

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 （Q3IY11） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （Q02762） 2-O-octyl-beta-D-glucopyranose × 2 PROTOPORPHYRIN IX CONTAINING FE × 6 STIGMATELLIN A × 2 (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE × 2 ;(2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE ; × 2 STRONTIUM ION × 2 FE2/S2 (INORGANIC) CLUSTER × 2 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Cytochrome c1 × 2 （Q3IY11） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （Q02762） 2-O-octyl-beta-D-glucopyranose × 2 PROTOPORPHYRIN IX CONTAINING FE × 6 STIGMATELLIN A × 2 (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE × 2 ;(2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE ; × 2 STRONTIUM ION × 4 FE2/S2 (INORGANIC) CLUSTER × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYB_RHOSH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–428； UniProt 3–430 Author chain D； PDBConstruct 1–428； UniProt 3–430 Author chain G； PDBConstruct 1–428； UniProt 3–430 Author chain J； PDBConstruct 1–428； UniProt 3–430

Cytochrome c1

Rhodobacter sphaeroides

UniProt Q3IY11

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 （Q02761） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （Q02762） 2-O-octyl-beta-D-glucopyranose × 2 PROTOPORPHYRIN IX CONTAINING FE × 6 STIGMATELLIN A × 2 (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE × 2 ;(2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE ; × 2 STRONTIUM ION × 2 FE2/S2 (INORGANIC) CLUSTER × 2 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Cytochrome b × 2 （Q02761） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （Q02762） 2-O-octyl-beta-D-glucopyranose × 2 PROTOPORPHYRIN IX CONTAINING FE × 6 STIGMATELLIN A × 2 (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE × 2 ;(2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE ; × 2 STRONTIUM ION × 4 FE2/S2 (INORGANIC) CLUSTER × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3IY11_RHOS4
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–256； UniProt 23–278 Author chain E； PDBConstruct 1–256； UniProt 23–278 Author chain H； PDBConstruct 1–256； UniProt 23–278 Author chain K； PDBConstruct 1–256； UniProt 23–278

Ubiquinol-cytochrome c reductase iron-sulfur subunit

Rhodobacter sphaeroides

UniProt Q02762

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 （Q02761） Cytochrome c1 × 2 （Q3IY11） 2-O-octyl-beta-D-glucopyranose × 2 PROTOPORPHYRIN IX CONTAINING FE × 6 STIGMATELLIN A × 2 (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE × 2 ;(2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE ; × 2 STRONTIUM ION × 2 FE2/S2 (INORGANIC) CLUSTER × 2 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Cytochrome b × 2 （Q02761） Cytochrome c1 × 2 （Q3IY11） 2-O-octyl-beta-D-glucopyranose × 2 PROTOPORPHYRIN IX CONTAINING FE × 6 STIGMATELLIN A × 2 (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE × 2 ;(2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE ; × 2 STRONTIUM ION × 4 FE2/S2 (INORGANIC) CLUSTER × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UCRI_RHOSH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–179； UniProt 9–187 Author chain F； PDBConstruct 1–179； UniProt 9–187 Author chain I； PDBConstruct 1–179； UniProt 9–187 Author chain L； PDBConstruct 1–179； UniProt 9–187

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	2qjp
Deposition date deposition_date	2007-07-08
Structure title title	Crystal structure of wild type rhodobacter sphaeroides with stigmatellin and antimycin inhibited
Keywords keywords	;Cytochrome b with 8 TM helices, one c-term TM in cytochrome c1 and an N-term TM in the iron-sulfur-protein (Rieske), Electron transport, Heme, Membrane, Metal-binding, Respiratory chain, Transmembrane, Transport, 2Fe-2S, Inner membrane, Oxidoreductase ;; 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.

2qjp__assembly_1__model_1

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

Download this curve (.dat)

2qjp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qjp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.63 Å
Rg (electron density)	37.27 Å
Total Rg	37.79 Å
Atom count	14008
Residues	1726
Excluded volume	252510 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qjp__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2qjp__assembly_2__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 (11)

Entity 1 Entity 1 polymer

Description description	Cytochrome b
Molecular weight formula_weight	48367.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	28227

GIPHDHYEPRTGIEKWLHSRLPIVALAYDTIMIPTPRNLNWMWIWGVVLAFCLVLQIVTGIVLAMHYTPHVDLAFASVEHIMRNVNGGFMLRYLHANGASLFFIAVYLHIFRGLYYGSYKAPREVTWIVGMLIYLAMMATAFMGYVLPWGQMSFWGATVITGLFGAIPGIGHSIQTWLLGGPAVDNATLNRFFSLHYLLPFVIAALVAIHIWAFHSTGNNNPTGVEVRRTSKAEAQKDTVPFWPYFIIKDVFALAVVLLVFFAIVGFMPNYLGHPDNYIEANPLSTPAHIVPEWYFLPFYAILRAFTADVWVVQIANFISFGIIDAKFFGVLAMFGAILVMALVPWLDTSPVRSGRYRPMFKIYFWLLAADFVILTWVGAQQTTFPYDWISLIASAYWFAYFLVILPILGAIEKPVAPPATIEEDFNA

Source Source

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

Entity 2 Entity 2 polymer

Description description	Cytochrome c1
Molecular weight formula_weight	27786.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

AGGGHVEDVPFSFEGPFGTFDQHQLQRGLQVYTEVCAACHGMKFVPIRSLSEPGGPELPEDQVRAYATQFTVTDEETGEDREGKPTDHFPHSALENAPDLSLMAKARAGFHGPMGTGISQLFNGIGGPEYIYSVLTGFPEEPPKCAEGHEPDGFYYNRAFQNGSVPDTCKDANGVKTTAGSWIAMPPPLMDDLVEYADGHDASVHAMAEDVSAFLMWAAEPKLMARKQAGFTAVMFLTVLSVLLYLTNKRLWAGVK

Source Source

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

Entity 3 Entity 3 polymer

Description description	Ubiquinol-cytochrome c reductase iron-sulfur subunit
Molecular weight formula_weight	19071.5 kDa
EC 编号 ec_number	1.10.2.2
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

GTRRDFLYYATAGAGAVATGAAVWPLINQMNPSADVQALASIFVDVSSVEPGVQLTVKFLGKPIFIRRRTEADIELGRSVQLGQLVDTNARNANIDAGAEATDQNRTLDEAGEWLVMWGVCTHLGCVPIGGVSGDFGGWFCPCHGSHYDSAGRIRKGPAPENLPIPLAKFIDETTIQLG

Source Source

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

Entity 4 Entity 4 non-polymer

Description description	2-O-octyl-beta-D-glucopyranose
Molecular weight formula_weight	292.4 kDa
Source method src_method	man
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 6 Entity 6 non-polymer

Description description	STIGMATELLIN A
Molecular weight formula_weight	514.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
Molecular weight formula_weight	661.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	;(2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE ;
Molecular weight formula_weight	548.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 non-polymer

Description description	STRONTIUM ION
Molecular weight formula_weight	87.6 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 10 Entity 10 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	209

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6. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

Domain ID domain_id	2qjpA00
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	2qjpB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	2qjpB02
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	100 — Cytochrome c1, transmembrane anchor, C-terminal

Domain ID domain_id	2qjpC01
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	2qjpC02
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	2qjpD00
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	2qjpE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	2qjpE02
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	100 — Cytochrome c1, transmembrane anchor, C-terminal

Domain ID domain_id	2qjpF01
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	2qjpF02
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	2qjpG00
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	2qjpH01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	2qjpH02
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	100 — Cytochrome c1, transmembrane anchor, C-terminal

Domain ID domain_id	2qjpI01
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	2qjpI02
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	2qjpJ00
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	2qjpK01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	2qjpK02
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	100 — Cytochrome c1, transmembrane anchor, C-terminal

Domain ID domain_id	2qjpL01
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	2qjpL02
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	135.061 Å
Unit-cell length b length_b	146.520 Å
Unit-cell length c length_c	141.003 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.21 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	17.980 Å
R factor r_factor	0.2440
R_work r_work	0.2440
R_free r_free	0.2770

Crystal structure of wild type rhodobacter sphaeroides with stigmatellin and antimycin inhibited

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

2qjp__assembly_1__model_1

2qjp__assembly_1__model_1 | I(q)

2qjp__assembly_1__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 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

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

6. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

7. Citations (1)