7tce

Crystal structure of delta sub IV Rhodobacter Sphaeroides bc1 with the antimalarial drug atovaquone.

Method: X-RAY DIFFRACTION

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

Cytochrome b

Cereibacter 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 （A3PFR5） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （Q02762） PROTOPORPHYRIN IX CONTAINING FE × 4 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione × 2 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE × 2 STRONTIUM ION × 4 octyl beta-D-glucopyranoside × 2 HEME C × 2 FE2/S2 (INORGANIC) CLUSTER × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Cytochrome c1 × 2 （A3PFR5） Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 （Q02762） PROTOPORPHYRIN IX CONTAINING FE × 4 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione × 2 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE × 2 STRONTIUM ION × 2 octyl beta-D-glucopyranoside × 2 HEME C × 2 FE2/S2 (INORGANIC) CLUSTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYB_CERSP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–445； UniProt 1–445 Author chain E； PDBConstruct 1–445； UniProt 1–445 Author chain K； PDBConstruct 1–445； UniProt 1–445 Author chain O； PDBConstruct 1–445； UniProt 1–445

Cytochrome c1

Cereibacter sphaeroides

UniProt A3PFR5

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 × 4 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione × 2 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE × 2 STRONTIUM ION × 4 octyl beta-D-glucopyranoside × 2 HEME C × 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 × 4 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione × 2 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE × 2 STRONTIUM ION × 2 octyl beta-D-glucopyranoside × 2 HEME C × 2 FE2/S2 (INORGANIC) CLUSTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A3PFR5_RHOS1
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–263； UniProt 23–285 Author chain F； PDBConstruct 1–263； UniProt 23–285 Author chain L； PDBConstruct 1–263； UniProt 23–285 Author chain P； PDBConstruct 1–263； UniProt 23–285

Ubiquinol-cytochrome c reductase iron-sulfur subunit

Cereibacter 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 （A3PFR5） PROTOPORPHYRIN IX CONTAINING FE × 4 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione × 2 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE × 2 STRONTIUM ION × 4 octyl beta-D-glucopyranoside × 2 HEME C × 2 FE2/S2 (INORGANIC) CLUSTER × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Cytochrome b × 2 （Q02761） Cytochrome c1 × 2 （A3PFR5） PROTOPORPHYRIN IX CONTAINING FE × 4 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione × 2 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE × 2 STRONTIUM ION × 2 octyl beta-D-glucopyranoside × 2 HEME C × 2 FE2/S2 (INORGANIC) CLUSTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UCRI_CERSP
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–187； UniProt 1–187 Author chain G； PDBConstruct 1–187； UniProt 1–187 Author chain M； PDBConstruct 1–187； UniProt 1–187 Author chain Q； 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_id	7tce
Deposition date deposition_date	2021-12-23
Structure title title	Crystal structure of delta sub IV Rhodobacter Sphaeroides bc1 with the antimalarial drug atovaquone.
Keywords keywords	Respiratory Chain Complex III, Anti-malarial Atovaquone, Rhodobacter Spaheroides bc1, Inhibition, MEMBRANE PROTEIN, 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.

7tce__assembly_2__model_1

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

Download this curve (.dat)

7tce__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7tce__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	38.76 Å
Rg (electron density)	37.43 Å
Total Rg	37.96 Å
Atom count	27340
Residues	1728
Excluded volume	249850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7tce__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7tce__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 (10)

Entity 1 Entity 1 polymer

Description description	Cytochrome b
Molecular weight formula_weight	50087.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,K,O
Atom count atom_count	54681

MSGIPHDHYEPRTGIEKWLHSRLPIVALAYDTIMIPTPRNLNWMWIWGVVLAFCLVLQIVTGIVLAMHYTPHVDLAFASVEHIMRNVNGGFMLRYLHANGASLFFIAVYLHIFRGLYYGSYKAPREVTWIVGMLIYLAMMATAFMGYVLPWGQMSFWGATVITGLFGAIPGIGHSIQTWLLGGPAVDNATLNRFFSLHYLLPFVIAALVAIHIWAFHSTGNNNPTGVEVRRTSKAEAQKDTVPFWPYFIIKDVFALAVVLLVFFAIVGFMPNYLGHPDNYIEANPLSTPAHIVPEWYFLPFYAILRAFTADVWVVQIANFISFGIIDAKFFGVLAMFGAILVMALVPWLDTSPVRSGRYRPMFKIYFWLLAADFVILTWVGAQQTTFPYDWISLIASAYWFAYFLVILPILGAIEKPVAPPATIEEDFNAHYSPATGGTKTVVAE

Source Source

Source organism organism	Cereibacter sphaeroides
Common name common_name	Rhodobacter sphaeroides
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	Cereibacter sphaeroides

Entity 2 Entity 2 polymer

Description description	Cytochrome c1
Molecular weight formula_weight	29374.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

AGGGHVEDVPFSFEGPFGTFDQHQLQRGLQVYTEVCAACHGMKFVPIRSLSEPGGPELPEDQVRAYATQFTVTDEETGEDREGKPTDHFPHSALENAPDLSLMAKARAGFHGPMGTGISQLFNGIGGPEYIYSVLTGFPEEPPKCAEGHEPDGFYYNRAFQNGSVPDTCKDANGVKTTAGSWIAMPPPLMDDLVEYADGHDASVHAMAEDVSAFLMWAAEPKLMARKQAGFTAVMFLTVLSVLLYLTNKRLWAGVKGKKKTNVHHHHHH

Source Source

Source organism organism	Cereibacter sphaeroides
Common name common_name	Rhodobacter sphaeroides
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	Cereibacter sphaeroides

Entity 3 Entity 3 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	man
Copy count entity_count	4

Polymer Polymer

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

MSNAEDHAGTRRDFLYYATAGAGAVATGAAVWPLINQMNPSADVQALASIFVDVSSVEPGVQLTVKFLGKPIFIRRRTEADIELGRSVQLGQLVDTNARNANIDAGAEATDQNRTLDEAGEWLVMWGVCTHLGCVPIGGVSGDFGGWFCPCHGSHYDSAGRIRKGPAPENLPIPLAKFIDETTIQLG

Source Source

Source organism organism	Cereibacter sphaeroides
Common name common_name	Rhodobacter sphaeroides
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	Cereibacter sphaeroides

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	8

Entity 5 Entity 5 non-polymer

Description description	2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione
Molecular weight formula_weight	366.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
Molecular weight formula_weight	410.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

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

Entity 8 Entity 8 non-polymer

Description description	octyl beta-D-glucopyranoside
Molecular weight formula_weight	292.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	4

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

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6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id	7tceA01
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	7tceC01
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	7tceE01
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	7tceG01
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	7tceK01
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	7tceM01
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	7tceQ01
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	127.273 Å
Unit-cell length b length_b	156.388 Å
Unit-cell length c length_c	141.407 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.67 °
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	3.850 Å
Low-resolution limit resolution_low	39.430 Å
R factor r_factor	0.2417
R_work r_work	0.2407
R_free r_free	0.2732

Crystal structure of delta sub IV Rhodobacter Sphaeroides bc1 with the antimalarial drug atovaquone.

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

7tce__assembly_2__model_1

7tce__assembly_2__model_1 | I(q)

7tce__assembly_2__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 (10)

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

6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

7. Citations (1)