8go3

Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent

Method: ELECTRON MICROSCOPY

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

Cytochrome bo(3) ubiquinol oxidase subunit 1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cytochrome bo(3) ubiquinol oxidase subunit 2 × 1 （P0ABJ1） ubiquinol oxidase × 1 （B6HZN6） Cytochrome bo(3) ubiquinol oxidase subunit 4 × 1 （C3TLX2） PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1 COPPER (II) ION × 1 Ubiquinone-8 × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B7MD89_ECO45
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–663； UniProt 1–663

Cytochrome bo(3) ubiquinol oxidase subunit 2

OrganismNot specified

UniProt P0ABJ1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cytochrome bo(3) ubiquinol oxidase subunit 1 × 1 （B7MD89） ubiquinol oxidase × 1 （B6HZN6） Cytochrome bo(3) ubiquinol oxidase subunit 4 × 1 （C3TLX2） PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1 COPPER (II) ION × 1 Ubiquinone-8 × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYOA_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–315； UniProt 1–315

ubiquinol oxidase

OrganismNot specified

UniProt B6HZN6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cytochrome bo(3) ubiquinol oxidase subunit 1 × 1 （B7MD89） Cytochrome bo(3) ubiquinol oxidase subunit 2 × 1 （P0ABJ1） Cytochrome bo(3) ubiquinol oxidase subunit 4 × 1 （C3TLX2） PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1 COPPER (II) ION × 1 Ubiquinone-8 × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B6HZN6_ECOSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–204； UniProt 1–204

Cytochrome bo(3) ubiquinol oxidase subunit 4

OrganismNot specified

UniProt C3TLX2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cytochrome bo(3) ubiquinol oxidase subunit 1 × 1 （B7MD89） Cytochrome bo(3) ubiquinol oxidase subunit 2 × 1 （P0ABJ1） ubiquinol oxidase × 1 （B6HZN6） PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1 COPPER (II) ION × 1 Ubiquinone-8 × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C3TLX2_ECOLX
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–109； UniProt 1–109

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	8go3
Deposition date deposition_date	2022-08-24
Last revision last_revision	2023-08-30
Structure title title	Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent
Keywords keywords	Cytochrome bo3, ubiquinol oxidase, DDM detergent, TRANSLOCASE; TRANSLOCASE
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.

8go3__assembly_1__model_1

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

Download this curve (.dat)

8go3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8go3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.42 Å
Rg (electron density)	31.05 Å
Total Rg	31.82 Å
Atom count	9739
Residues	1203
Excluded volume	178500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8go3__assembly_1__model_1`	tetrameric （4）	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	Cytochrome bo(3) ubiquinol oxidase subunit 1
Molecular weight formula_weight	74424.5 kDa
EC 编号 ec_number	7.1.1.3
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9739

MFGKLSLDAVPFHEPIVMVTIAGIILGGLALVGLITYFGKWTYLWKEWLTSVDHKRLGIMYIIVAIVMLLRGFADAIMMRSQQALASAGEAGFLPPHHYDQIFTAHGVIMIFFVAMPFVIGLMNLVVPLQIGARDVAFPFLNNLSFWFTVVGVILVNVSLGVGEFAQTGWLAYPPLSGIEYSPGVGVDYWIWSLQLSGIGTTLTGINFFVTILKMRAPGMTMFKMPVFTWASLCANVLIIASFPILTVTVALLTLDRYLGTHFFTNDMGGNMMMYINLIWAWGHPEVYILILPVFGVFSEIAATFSRKRLFGYTSLVWATVCITVLSFIVWLHHFFTMGAGANVNAFFGITTMIIAIPTGVKIFNWLFTMYQGRIVFHSAMLWTIGFIVTFSVGGMTGVLLAVPGADFVLHNSLFLIAHFHNVIIGGVVFGCFAGMTYWWPKAFGFKLNETWGKRAFWFWIIGFFVAFMPLYALGFMGMTRRLSQQIDPQFHTMLMIAASGAVLIALGILCLVIQMYVSIRDRDQNRDLTGDPWGGRTLEWATSSPPPFYNFAVVPHVHERDAFWEMKEKGEAYKKPDHYEEIHMPKNSGAGIVIAAFSTIFGFAMIWHIWWLAIVGFAGMIITWIVKSFDEDVDYYVPVAEIEKLENQHFDEITKAGLKNGN

Entity 2 Entity 2 polymer

Description description	Cytochrome bo(3) ubiquinol oxidase subunit 2
Molecular weight formula_weight	34947.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MRLRKYNKSLGWLSLFAGTVLLSGCNSALLDPKGQIGLEQRSLILTAFGLMLIVVIPAILMAVGFAWKYRASNKDAKYSPNWSHSNKVEAVVWTVPILIIIFLAVLTWKTTHALEPSKPLAHDEKPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANTPVYFKVTSNSVMNSFFIPRLGSQIYAMAGMQTRLHLIANEPGTYDGISASYSGPGFSGMKFKAIATPDRAAFDQWVAKAKQSPNTMSDMAAFEKLAAPSEYNQVEYFSNVKPDLFADVINKFMAHGKSMDMTQPEGEHSAHEGMEGMDMSHAESAH

Entity 3 Entity 3 polymer

Description description	ubiquinol oxidase
Molecular weight formula_weight	22642.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MATDTLTHATAHAHEHGHHDAGGTKIFGFWIYLMSDCILFSILFATYAVLVNGTAGGPTGKDIFELPFVLVETFLLLFSSITYGMAAIAMYKNNKSQVISWLALTWLFGAGFIGMEIYEFHHLIVNGMGPDRSGFLSAFFALVGTHGLHVTSGLIWMAVLMVQIARRGLTSTNRTRIMCLSLFWHFLDVVWICVFTVVYLMGAM

Entity 4 Entity 4 polymer

Description description	Cytochrome bo(3) ubiquinol oxidase subunit 4
Molecular weight formula_weight	12037.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MSHSTDHSGASHGSVKTYMTGFILSIILTVIPFWMVMTGAASPAVILGTILAMAVVQVLVHLVCFLHMNTKSDEGWNMTAFVFTVLIIAILVVGSIWIMWNLNYNMMMH

Entity 5 Entity 5 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	HEME O
Molecular weight formula_weight	838.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	Ubiquinone-8
Molecular weight formula_weight	727.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	1,2-Distearoyl-sn-glycerophosphoethanolamine
Molecular weight formula_weight	748.1 kDa
Source method src_method	syn
Copy count entity_count	2

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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	triclinic

Resolution resolution	3.09 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	538627

Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent

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

Cytochrome bo(3) ubiquinol oxidase subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Cytochrome bo(3) ubiquinol oxidase subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

ubiquinol oxidase

State in the Current Structure

Other States of the Same Protein in the Database

Cytochrome bo(3) ubiquinol oxidase subunit 4

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

8go3__assembly_1__model_1

8go3__assembly_1__model_1 | I(q)

8go3__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

7. Citations (1)

Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent

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

Cytochrome bo(3) ubiquinol oxidase subunit 1

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 bo(3) ubiquinol oxidase subunit 2

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 oxidase

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 bo(3) ubiquinol oxidase subunit 4

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

8go3__assembly_1__model_1

8go3__assembly_1__model_1 | I(q)

8go3__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

7. Citations (1)