2yiu

X-ray structure of the dimeric cytochrome BC1 complex from the soil bacterium paracoccus denitrificans at 2.7 angstrom resolution

Method: X-RAY DIFFRACTION

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

CYTOCHROME B

OrganismNot specified

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, HEME PROTEIN × 2 （P13627） UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT × 2 （P05417） PROTOPORPHYRIN IX CONTAINING FE × 4 STIGMATELLIN A × 2 HEME C × 2 FE2/S2 (INORGANIC) CLUSTER × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYB_PARDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–440； UniProt 1–440 Author chain D； PDBConstruct 1–440； UniProt 1–440

CYTOCHROME C1, HEME PROTEIN

OrganismNot specified

UniProt P13627

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 （P05418） UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT × 2 （P05417） PROTOPORPHYRIN IX CONTAINING FE × 4 STIGMATELLIN A × 2 HEME C × 2 FE2/S2 (INORGANIC) CLUSTER × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CY1_PARDE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–14； UniProt 25–38 Author chain B； PDBConstruct 15–263； UniProt 202–450 Author chain E； PDBConstruct 1–14； UniProt 25–38 Author chain E； PDBConstruct 15–263； UniProt 202–450

UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT

OrganismNot specified

UniProt P05417

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 （P05418） CYTOCHROME C1, HEME PROTEIN × 2 （P13627） PROTOPORPHYRIN IX CONTAINING FE × 4 STIGMATELLIN A × 2 HEME C × 2 FE2/S2 (INORGANIC) CLUSTER × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UCRI_PARDE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–190； UniProt 1–190 Author chain F； PDBConstruct 1–190； UniProt 1–190

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	2yiu
Deposition date deposition_date	2011-05-16
Structure title title	X-ray structure of the dimeric cytochrome BC1 complex from the soil bacterium paracoccus denitrificans at 2.7 angstrom resolution
Keywords keywords	OXIDOREDUCTASE; OXIDOREDUCTASE
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.

2yiu__assembly_1__model_1

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

Download this curve (.dat)

2yiu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yiu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.91 Å
Rg (electron density)	36.64 Å
Total Rg	37.12 Å
Atom count	12984
Residues	1616
Excluded volume	234050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yiu__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 (8)

Entity 1 Entity 1 polymer

Description description	CYTOCHROME B
Molecular weight formula_weight	51536.2 kDa
EC 编号 ec_number	1.10.2.2
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	12990

MAGIPHDHYEPKTGFERWLHRRLPIVSLVYDTLMIPTPKNLNWWWIWGIVLAFCLVLQIATGIVLVMHYTPHVDLAFASVEHIMRDVNGGYMLRYLHANGASLFFLAVYIHIFRGLYYGSYKAPREVTWIVGMLIYLMMMGTAFMGYVLPWGQMSFWGATVITGLFGAIPGVGEAIQTWLLGGPAVDNPTLNRFFSLHYLLPFVIAALVVVHIWAFHTTGNNNPTGVEVRRGSKEEAKKDTLPFWPYFVIKDLFALAVVLVVFFAIVGFMPNYLGHPDNYIEANPLVTPAHIVPEWYFLPFYAILRAFTADVWVVMLVNWLSFGIIDAKFFGVIAMFGAILVMALVPWLDTSRVRSGQYRPLFKWWFWLLAVDFVVLMWVGAMPAEGIYPYIALAGSAYWFAYFLIILPLLGIIEKPDAMPQTIEEDFNAHYGPETHPAEHHHHHHHHHH

Entity 2 Entity 2 polymer

Description description	CYTOCHROME C1, HEME PROTEIN
Molecular weight formula_weight	28491.7 kDa
EC 编号 ec_number	1.10.2.2
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

QDASTAPGTTAPAGAAQEAGDSHAAAHIEDISFSFEGPFGKFDQHQLQRGLQVYTEVCSACHGLRYVPLRTLADEGGPQLPEDQVRAYAANFDITDPETEEDRPRVPTDHFPTVSGEGMGPDLSLMAKARAGFHGPYGTGLSQLFNGIGGPEYIHAVLTGYDGEEKEEAGAVLYHNAAFAGNWIQMAAPLSDDQVTYEDGTPATVDQMATDVAAFLMWTAEPKMMDRKQVGFVSVIFLIVLAALLYLTNKKLWQPIKHPRKPE

Entity 3 Entity 3 polymer

Description description	UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT
Molecular weight formula_weight	20321.5 kDa
EC 编号 ec_number	1.10.2.2
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MSHADEHAGDHGATRRDFLYYATAGAGTVAAGAAAWTLVNQMNPSADVQALASIQVDVSGVETGTQLTVKWLGKPVFIRRRTEDEIQAGREVDLGQLIDRSAQNSNKPDAPATDENRTMDEAGEWLVMIGVCTHLGCVPIGDGAGDFGGWFCPCHGSHYDTSGRIRRGPAPQNLHIPVAEFLDDTTIKLG

Entity 4 Entity 4 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
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	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 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 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	6

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6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id	2yiuA00
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	2yiuB01
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	2yiuB02
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	2yiuC01
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	2yiuC02
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	2yiuD00
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	2yiuE01
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	2yiuE02
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	2yiuF00
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	85.300 Å
Unit-cell length b length_b	164.910 Å
Unit-cell length c length_c	100.610 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.18 °
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	2.700 Å
Low-resolution limit resolution_low	97.960 Å
R factor r_factor	0.2403
R_work r_work	0.2377
R_free r_free	0.2905

X-ray structure of the dimeric cytochrome BC1 complex from the soil bacterium paracoccus denitrificans at 2.7 angstrom resolution

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, HEME PROTEIN

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

2yiu__assembly_1__model_1

2yiu__assembly_1__model_1 | I(q)

2yiu__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

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 water

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)

X-ray structure of the dimeric cytochrome BC1 complex from the soil bacterium paracoccus denitrificans at 2.7 angstrom resolution

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, HEME PROTEIN

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

2yiu__assembly_1__model_1

2yiu__assembly_1__model_1 | I(q)

2yiu__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

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 water

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)