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2fyn

Crystal Structure Analysis of the double mutant Rhodobacter Sphaeroides bc1 complex

Method: X-RAY DIFFRACTION
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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 （Q02760） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （Q02762） 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 FE2/S2 (INORGANIC) CLUSTER × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 Cytochrome c1 × 2 （Q02760） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （Q02762） 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 FE2/S2 (INORGANIC) CLUSTER × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 6 Cytochrome c1 × 2 （Q02760） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （Q02762） 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 FE2/S2 (INORGANIC) CLUSTER × 2 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 2–445； UniProt 1–444 Author chain D； PDBConstruct 2–445； UniProt 1–444 Author chain G； PDBConstruct 2–445； UniProt 1–444 Author chain J； PDBConstruct 2–445； UniProt 1–444 Author chain M； PDBConstruct 2–445； UniProt 1–444 Author chain P； PDBConstruct 2–445； UniProt 1–444

Cytochrome c1

Rhodobacter sphaeroides

UniProt Q02760

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） 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 FE2/S2 (INORGANIC) CLUSTER × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 Cytochrome b × 2 （Q02761） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （Q02762） 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 FE2/S2 (INORGANIC) CLUSTER × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 6 Cytochrome b × 2 （Q02761） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （Q02762） 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 FE2/S2 (INORGANIC) CLUSTER × 2 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 5kkz 5kkz 5kli 5kli 7tlj

8 assemblies

View Construct and Data Evidence
UniProt name CY1_RHOSH
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 （Q02760） 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 FE2/S2 (INORGANIC) CLUSTER × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 Cytochrome b × 2 （Q02761） Cytochrome c1 × 2 （Q02760） 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 FE2/S2 (INORGANIC) CLUSTER × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 6 Cytochrome b × 2 （Q02761） Cytochrome c1 × 2 （Q02760） 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 FE2/S2 (INORGANIC) CLUSTER × 2 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id2fyn
Deposition date deposition_date2006-02-08
Structure title titleCrystal Structure Analysis of the double mutant Rhodobacter Sphaeroides bc1 complex
Keywords keywordsTransmembrane helices, functional dimer, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-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.

2fyn__assembly_2__model_1

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

Download this curve (.dat)

2fyn__assembly_2__model_1 | I(q)

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

2fyn__assembly_2__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）38.75 Å
Rg (electron density)37.41 Å
Total Rg37.93 Å
Atom count13896
Residues1726
Excluded volume250110 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2fyn__assembly_1__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2fyn__assembly_2__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 2fyn__assembly_3__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 (7)

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6. Fold Classification (SCOP + CATH) 30 domains

CATH v4.4 (30 domains)

Domain ID domain_id2fynA00
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_id2fynB01
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_id2fynB02
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_id2fynC01
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_id2fynC02
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_id2fynD00
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_id2fynE01
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_id2fynE02
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_id2fynF01
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_id2fynF02
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_id2fynG00
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_id2fynH01
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_id2fynH02
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_id2fynI01
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_id2fynI02
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_id2fynJ00
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_id2fynK01
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_id2fynK02
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_id2fynL01
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_id2fynL02
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_id2fynM00
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_id2fynN01
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_id2fynN02
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_id2fynO01
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_id2fynO02
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_id2fynP00
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_id2fynQ01
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_id2fynQ02
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_id2fynR01
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_id2fynR02
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
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7. Citations (1)