← Back to search
2qjy

Crystal structure of rhodobacter sphaeroides double mutant with stigmatellin and UQ2

Method: X-RAY DIFFRACTION
▼

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

Cytochrome b

Rhodobacter sphaeroides

UniProt Q02761

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） STRONTIUM ION × 3 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 UBIQUINONE-2 × 2 2-O-octyl-beta-D-glucopyranose × 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） STRONTIUM ION × 3 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 UBIQUINONE-2 × 2 2-O-octyl-beta-D-glucopyranose × 2 FE2/S2 (INORGANIC) CLUSTER × 2 CHLORIDE ION × 1 water × 6 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 6 Cytochrome c1 × 2 （Q3IY11） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （Q02762） STRONTIUM ION × 3 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 UBIQUINONE-2 × 2 2-O-octyl-beta-D-glucopyranose × 2 FE2/S2 (INORGANIC) CLUSTER × 2 CHLORIDE ION × 1 SODIUM ION × 1 water × 6 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2fyn 2fyn 2fyn 2qjk 2qjk 2qjk 2qjp 2qjp 2qjy 2qjy 2qjy 5kkz

18 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CYB_RHOSH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–445； UniProt 1–445 Author chain D； PDBConstruct 1–445； UniProt 1–445 Author chain G； PDBConstruct 1–445； UniProt 1–445 Author chain J； PDBConstruct 1–445； UniProt 1–445 Author chain M； PDBConstruct 1–445； UniProt 1–445 Author chain P； PDBConstruct 1–445； UniProt 1–445

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） STRONTIUM ION × 3 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 UBIQUINONE-2 × 2 2-O-octyl-beta-D-glucopyranose × 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） STRONTIUM ION × 3 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 UBIQUINONE-2 × 2 2-O-octyl-beta-D-glucopyranose × 2 FE2/S2 (INORGANIC) CLUSTER × 2 CHLORIDE ION × 1 water × 6 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 6 Cytochrome b × 2 （Q02761） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （Q02762） STRONTIUM ION × 3 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 UBIQUINONE-2 × 2 2-O-octyl-beta-D-glucopyranose × 2 FE2/S2 (INORGANIC) CLUSTER × 2 CHLORIDE ION × 1 SODIUM ION × 1 water × 6 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2qjk 2qjk 2qjk 2qjp 2qjp 2qjy 2qjy 2qjy 8asi 8asj

10 assemblies

View Construct and Data Evidence
UniProt name Q3IY11_RHOS4
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–263； UniProt 23–285 Author chain E； PDBConstruct 1–263； UniProt 23–285 Author chain H； PDBConstruct 1–263； UniProt 23–285 Author chain K； PDBConstruct 1–263； UniProt 23–285 Author chain N； PDBConstruct 1–263； UniProt 23–285 Author chain Q； PDBConstruct 1–263； UniProt 23–285

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） STRONTIUM ION × 3 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 UBIQUINONE-2 × 2 2-O-octyl-beta-D-glucopyranose × 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） STRONTIUM ION × 3 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 UBIQUINONE-2 × 2 2-O-octyl-beta-D-glucopyranose × 2 FE2/S2 (INORGANIC) CLUSTER × 2 CHLORIDE ION × 1 water × 6 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 6 Cytochrome b × 2 （Q02761） Cytochrome c1 × 2 （Q3IY11） STRONTIUM ION × 3 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 UBIQUINONE-2 × 2 2-O-octyl-beta-D-glucopyranose × 2 FE2/S2 (INORGANIC) CLUSTER × 2 CHLORIDE ION × 1 SODIUM ION × 1 water × 6 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2nuk 2num 2nve 2nvf 2nvg 2nwf

6 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2fyn 2fyn 2fyn 2qjk 2qjk 2qjk 2qjp 2qjp 2qjy 2qjy 2qjy 5kkz

18 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UCRI_RHOSH
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–187； UniProt 1–187 Author chain F； PDBConstruct 1–187； UniProt 1–187 Author chain I； PDBConstruct 1–187； UniProt 1–187 Author chain L； PDBConstruct 1–187； UniProt 1–187 Author chain O； PDBConstruct 1–187； UniProt 1–187 Author chain R； PDBConstruct 1–187； UniProt 1–187

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id2qjy
Deposition date deposition_date2007-07-09
Structure title titleCrystal structure of rhodobacter sphaeroides double mutant with stigmatellin and UQ2
Keywords keywordsCytochrome B, 8 TM helixces Cytochrome C1, 1 c-term TM helix Rieske, 1 N-term TM helix, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
▼

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.

2qjy__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2qjy__assembly_3__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2qjy__assembly_3__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）38.73 Å
Rg (electron density)37.36 Å
Total Rg37.91 Å
Atom count13987
Residues1726
Excluded volume252190 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2qjy__assembly_1__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2qjy__assembly_2__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 2qjy__assembly_3__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (13)

▼

6. Fold Classification (SCOP + CATH) 30 domains

CATH v4.4 (30 domains)

Domain ID domain_id2qjyA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology810 — Cytochrome Bc1 Complex; Chain C
Homologous superfamily homologous superfamily10 — Cytochrome Bc1 Complex; Chain C
Domain ID domain_id2qjyB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2qjyB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily100 — Cytochrome c1, transmembrane anchor, C-terminal
Domain ID domain_id2qjyC01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily510 — Single helix bin
Domain ID domain_id2qjyC02
Class class2 — Mainly Beta
Architecture architecture102 — 3-layer Sandwich
Topology topology10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily10 — Rieske [2Fe-2S] iron-sulphur domain
Domain ID domain_id2qjyD00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology810 — Cytochrome Bc1 Complex; Chain C
Homologous superfamily homologous superfamily10 — Cytochrome Bc1 Complex; Chain C
Domain ID domain_id2qjyE01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2qjyE02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily100 — Cytochrome c1, transmembrane anchor, C-terminal
Domain ID domain_id2qjyF01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily510 — Single helix bin
Domain ID domain_id2qjyF02
Class class2 — Mainly Beta
Architecture architecture102 — 3-layer Sandwich
Topology topology10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily10 — Rieske [2Fe-2S] iron-sulphur domain
Domain ID domain_id2qjyG00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology810 — Cytochrome Bc1 Complex; Chain C
Homologous superfamily homologous superfamily10 — Cytochrome Bc1 Complex; Chain C
Domain ID domain_id2qjyH01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2qjyH02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily100 — Cytochrome c1, transmembrane anchor, C-terminal
Domain ID domain_id2qjyI01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily510 — Single helix bin
Domain ID domain_id2qjyI02
Class class2 — Mainly Beta
Architecture architecture102 — 3-layer Sandwich
Topology topology10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily10 — Rieske [2Fe-2S] iron-sulphur domain
Domain ID domain_id2qjyJ00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology810 — Cytochrome Bc1 Complex; Chain C
Homologous superfamily homologous superfamily10 — Cytochrome Bc1 Complex; Chain C
Domain ID domain_id2qjyK01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2qjyK02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily100 — Cytochrome c1, transmembrane anchor, C-terminal
Domain ID domain_id2qjyL01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily510 — Single helix bin
Domain ID domain_id2qjyL02
Class class2 — Mainly Beta
Architecture architecture102 — 3-layer Sandwich
Topology topology10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily10 — Rieske [2Fe-2S] iron-sulphur domain
Domain ID domain_id2qjyM00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology810 — Cytochrome Bc1 Complex; Chain C
Homologous superfamily homologous superfamily10 — Cytochrome Bc1 Complex; Chain C
Domain ID domain_id2qjyN01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2qjyN02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily100 — Cytochrome c1, transmembrane anchor, C-terminal
Domain ID domain_id2qjyO01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily510 — Single helix bin
Domain ID domain_id2qjyO02
Class class2 — Mainly Beta
Architecture architecture102 — 3-layer Sandwich
Topology topology10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily10 — Rieske [2Fe-2S] iron-sulphur domain
Domain ID domain_id2qjyP00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology810 — Cytochrome Bc1 Complex; Chain C
Homologous superfamily homologous superfamily10 — Cytochrome Bc1 Complex; Chain C
Domain ID domain_id2qjyQ01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2qjyQ02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily100 — Cytochrome c1, transmembrane anchor, C-terminal
Domain ID domain_id2qjyR01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily510 — Single helix bin
Domain ID domain_id2qjyR02
Class class2 — Mainly Beta
Architecture architecture102 — 3-layer Sandwich
Topology topology10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily10 — Rieske [2Fe-2S] iron-sulphur domain
▶

7. Citations (1)