8asj

Four subunit cytochrome b-c1 complex from Rhodobacter sphaeroides in native nanodiscs - focussed refinement in the b-c conformation

Method: ELECTRON MICROSCOPY

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

Ubiquinol-cytochrome c reductase iron-sulfur subunit

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Cytochrome b × 2 （Q3IY10） Cytochrome c1 × 2 （Q3IY11） Cytochrome b-c1 subunit IV × 2 （Q3J2Z2） FE2/S2 (INORGANIC) CLUSTER × 2 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 12 PROTOPORPHYRIN IX CONTAINING FE × 4 HEME C × 2 UBIQUINONE-10 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3IY09_CERS4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–187； UniProt 1–187 Author chain E； PDBConstruct 1–187； UniProt 1–187

Cytochrome b

OrganismNot specified

UniProt Q3IY10

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （Q3IY09） Cytochrome c1 × 2 （Q3IY11） Cytochrome b-c1 subunit IV × 2 （Q3J2Z2） FE2/S2 (INORGANIC) CLUSTER × 2 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 12 PROTOPORPHYRIN IX CONTAINING FE × 4 HEME C × 2 UBIQUINONE-10 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3IY10_CERS4
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–445； UniProt 1–445 Author chain F； PDBConstruct 1–445； UniProt 1–445

Cytochrome c1

OrganismNot specified

UniProt Q3IY11

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （Q3IY09） Cytochrome b × 2 （Q3IY10） Cytochrome b-c1 subunit IV × 2 （Q3J2Z2） FE2/S2 (INORGANIC) CLUSTER × 2 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 12 PROTOPORPHYRIN IX CONTAINING FE × 4 HEME C × 2 UBIQUINONE-10 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3IY11_CERS4
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–285； UniProt 1–285 Author chain G； PDBConstruct 1–285； UniProt 1–285

Cytochrome b-c1 subunit IV

OrganismNot specified

UniProt Q3J2Z2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （Q3IY09） Cytochrome b × 2 （Q3IY10） Cytochrome c1 × 2 （Q3IY11） FE2/S2 (INORGANIC) CLUSTER × 2 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 12 PROTOPORPHYRIN IX CONTAINING FE × 4 HEME C × 2 UBIQUINONE-10 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3J2Z2_CERS4
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–124； UniProt 1–124 Author chain H； PDBConstruct 1–124； UniProt 1–124

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	8asj
Deposition date deposition_date	2022-08-19
Structure title title	Four subunit cytochrome b-c1 complex from Rhodobacter sphaeroides in native nanodiscs - focussed refinement in the b-c conformation
Keywords keywords	cyt bc1 complex III membrane protein electron transport quinone cytochrome, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	ELECTRON MICROSCOPY

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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.

8asj__assembly_1__model_1

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

Download this curve (.dat)

8asj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8asj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.50 Å
Rg (electron density)	37.99 Å
Total Rg	38.51 Å
Atom count	14720
Residues	1789
Excluded volume	266030 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8asj__assembly_1__model_1`	octameric （8）	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	Ubiquinol-cytochrome c reductase iron-sulfur subunit
Molecular weight formula_weight	19928.4 kDa
EC 编号 ec_number	7.1.1.8
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	14720

MSNAEDHAGTRRDFLYYATAGAGAVATGAAVWPLINQMNPSADVQALASIFVDVSSVEPGVQLTVKFLGKPIFIRRRTEADIELGRSVQLGQLVDTNARNANIDAGAEATDQNRTLDEAGEWLVMWGVCTHLGCVPIGGVSGDFGGWFCPCHGSHYDSAGRIRKGPAPENLPIPLAKFIDETTIQLG

Entity 2 Entity 2 polymer

Description description	Cytochrome b
Molecular weight formula_weight	50087.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MSGIPHDHYEPRTGIEKWLHSRLPIVALAYDTIMIPTPRNLNWMWIWGVVLAFCLVLQIVTGIVLAMHYTPHVDLAFASVEHIMRNVNGGFMLRYLHANGASLFFIAVYLHIFRGLYYGSYKAPREVTWIVGMLIYLAMMATAFMGYVLPWGQMSFWGATVITGLFGAIPGIGHSIQTWLLGGPAVDNATLNRFFSLHYLLPFVIAALVAIHIWAFHSTGNNNPTGVEVRRTSKAEAQKDTVPFWPYFIIKDVFALAVVLLVFFAIVGFMPNYLGHPDNYIEANPLSTPAHIVPEWYFLPFYAILRAFTADVWVVQIANFISFGIIDAKFFGVLAMFGAILVMALVPWLDTSPVRSGRYRPMFKIYFWLLAADFVILTWVGAQQTTFPYDWISLIASAYWFAYFLVILPILGAIEKPVAPPATIEEDFNAHYSPATGGTKTVVAE

Entity 3 Entity 3 polymer

Description description	Cytochrome c1
Molecular weight formula_weight	30661.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MIRKLTLTAATALALSGGAAMAAGGGHVEDVPFSFEGPFGTFDQHQLQRGLQVYTEVCAACHGMKFVPIRSLSEPGGPELPEDQVRAYATQFTVTDEETGEDREGKPTDHFPHSALENAPDLSLMAKARAGFHGPMGTGISQLFNGIGGPEYIYSVLTGFPEEPPKCAEGHEPDGFYYNRAFQNGSVPDTCKDANGVKTTAGSWIAMPPPLMDDLVEYADGHDASVHAMAEDVSAFLMWAAEPKLMARKQAGFTAVMFLTVLSVLLYLTNKRLWAGVKGKKKTNV

Entity 4 Entity 4 polymer

Description description	Cytochrome b-c1 subunit IV
Molecular weight formula_weight	14415.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MFSFIDDIPSFEQIKARVRDDLRKHGWEKRWNDSRLVQKSRELLNDEELKIDPATWIWKRMPSREEVAARRQRDFETVWKYRYRLGGFASGALLALALAGIFSTGNFGGSSDAGNRPSVVYPIE

Entity 5 Entity 5 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 6 Entity 6 non-polymer

Description description	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
Molecular weight formula_weight	744.0 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 7 Entity 7 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 8 Entity 8 non-polymer

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

Entity 9 Entity 9 non-polymer

Description description	UBIQUINONE-10
Molecular weight formula_weight	863.3 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	8asjA01
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	8asjB01
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	8asjF01
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

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Resolution resolution	3.75 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	72118

Four subunit cytochrome b-c1 complex from Rhodobacter sphaeroides in native nanodiscs - focussed refinement in the b-c conformation

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

Ubiquinol-cytochrome c reductase iron-sulfur subunit

State in the Current Structure

Other States of the Same Protein in the Database

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

Cytochrome b-c1 subunit IV

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

8asj__assembly_1__model_1

8asj__assembly_1__model_1 | I(q)

8asj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

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 polymer

Polymer 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) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Four subunit cytochrome b-c1 complex from Rhodobacter sphaeroides in native nanodiscs - focussed refinement in the b-c conformation

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

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

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

Cytochrome b-c1 subunit IV

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

8asj__assembly_1__model_1

8asj__assembly_1__model_1 | I(q)

8asj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

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 polymer

Polymer 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) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)