6wti

The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli

Method: ELECTRON MICROSCOPY

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

Cytochrome o ubiquinol oxidase, subunit I

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Ubiquinol oxidase subunit 2 × 1 （A0A024L5V9） Cytochrome o ubiquinol oxidase × 1 （D6I7E4） Cytochrome o ubiquinol oxidase, subunit IV × 1 （I2RK84） PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1 COPPER (II) ION × 1 Ubiquinone-8 × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 9 pentadecyl(tetradecyl)peroxyanhydride × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4KCU1_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–663； UniProt 1–663

Ubiquinol oxidase subunit 2

Escherichia coli

UniProt A0A024L5V9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cytochrome o ubiquinol oxidase, subunit I × 1 （H4KCU1） Cytochrome o ubiquinol oxidase × 1 （D6I7E4） Cytochrome o ubiquinol oxidase, subunit IV × 1 （I2RK84） PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1 COPPER (II) ION × 1 Ubiquinone-8 × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 9 pentadecyl(tetradecyl)peroxyanhydride × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A024L5V9_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–315； UniProt 1–315

Cytochrome o ubiquinol oxidase

Escherichia coli

UniProt D6I7E4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cytochrome o ubiquinol oxidase, subunit I × 1 （H4KCU1） Ubiquinol oxidase subunit 2 × 1 （A0A024L5V9） Cytochrome o ubiquinol oxidase, subunit IV × 1 （I2RK84） PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1 COPPER (II) ION × 1 Ubiquinone-8 × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 9 pentadecyl(tetradecyl)peroxyanhydride × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D6I7E4_ECOLX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–204； UniProt 1–204

Cytochrome o ubiquinol oxidase, subunit IV

Escherichia coli

UniProt I2RK84

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cytochrome o ubiquinol oxidase, subunit I × 1 （H4KCU1） Ubiquinol oxidase subunit 2 × 1 （A0A024L5V9） Cytochrome o ubiquinol oxidase × 1 （D6I7E4） PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1 COPPER (II) ION × 1 Ubiquinone-8 × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 9 pentadecyl(tetradecyl)peroxyanhydride × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	I2RK84_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	6wti
Deposition date deposition_date	2020-05-02
Structure title title	The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli
Keywords keywords	ubiquinol oxidase cytochrome bo3, membrane protein, 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.

6wti__assembly_1__model_1

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

Download this curve (.dat)

6wti__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6wti__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.02 Å
Rg (electron density)	31.52 Å
Total Rg	32.31 Å
Atom count	9980
Residues	1207
Excluded volume	183740 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6wti__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 (10)

Entity 1 Entity 1 polymer

Description description	Cytochrome o ubiquinol oxidase, subunit I
Molecular weight formula_weight	74424.5 kDa
EC 编号 ec_number	1.10.3.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9980

MFGKLSLDAVPFHEPIVMVTIAGIILGGLALVGLITYFGKWTYLWKEWLTSVDHKRLGIMYIIVAIVMLLRGFADAIMMRSQQALASAGEAGFLPPHHYDQIFTAHGVIMIFFVAMPFVIGLMNLVVPLQIGARDVAFPFLNNLSFWFTVVGVILVNVSLGVGEFAQTGWLAYPPLSGIEYSPGVGVDYWIWSLQLSGIGTTLTGINFFVTILKMRAPGMTMFKMPVFTWASLCANVLIIASFPILTVTVALLTLDRYLGTHFFTNDMGGNMMMYINLIWAWGHPEVYILILPVFGVFSEIAATFSRKRLFGYTSLVWATVCITVLSFIVWLHHFFTMGAGANVNAFFGITTMIIAIPTGVKIFNWLFTMYQGRIVFHSAMLWTIGFIVTFSVGGMTGVLLAVPGADFVLHNSLFLIAHFHNVIIGGVVFGCFAGMTYWWPKAFGFKLNETWGKRAFWFWIIGFFVAFMPLYALGFMGMTRRLSQQIDPQFHTMLMIAASGAVLIALGILCLVIQMYVSIRDRDQNRDLTGDPWGGRTLEWATSSPPPFYNFAVVPHVHERDAFWEMKEKGEAYKKPDHYEEIHMPKNSGAGIVIAAFSTIFGFAMIWHIWWLAIVGFAGMIITWIVKSFDEDVDYYVPVAEIEKLENQHFDEITKAGLKNGN

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquinol oxidase subunit 2
Molecular weight formula_weight	34947.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MRLRKYNKSLGWLSLFAGTVLLSGCNSALLDPKGQIGLEQRSLILTAFGLMLIVVIPAILMAVGFAWKYRASNKDAKYSPNWSHSNKVEAVVWTVPILIIIFLAVLTWKTTHALEPSKPLAHDEKPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANTPVYFKVTSNSVMNSFFIPRLGSQIYAMAGMQTRLHLIANEPGTYDGISASYSGPGFSGMKFKAIATPDRAAFDQWVAKAKQSPNTMSDMAAFEKLAAPSEYNQVEYFSNVKPDLFADVINKFMAHGKSMDMTQPEGEHSAHEGMEGMDMSHAESAH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

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

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MATDTLTHATAHAHEHGHHDAGGTKIFGFWIYLMSDCILFSILFATYAVLVNGTAGGPTGKDIFELPFVLVETFLLLFSSITYGMAAIAMYKNNKSQVISWLALTWLFGAGFIGMEIYEFHHLIVNGMGPDRSGFLSAFFALVGTHGLHVTSGLIWMAVLMVQIARRGLTSTNRTRIMCLSLFWHFLDVVWICVFTVVYLMGAM

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Cytochrome o ubiquinol oxidase, subunit IV
Molecular weight formula_weight	12037.4 kDa
EC 编号 ec_number	1.10.3.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MSHSTDHSGASHGSVKTYMTGFILSIILTVIPFWMVMTGAASPAVILGTILAMAVVQVLVHLVCFLHMNTKSDEGWNMTAFVFTVLIIAILVVGSIWIMWNLNYNMMMH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

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	9

Entity 10 Entity 10 non-polymer

Description description	pentadecyl(tetradecyl)peroxyanhydride
Molecular weight formula_weight	524.9 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6wtib1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.17 — Transmembrane helix hairpin
Superfamily Superfamily superfamily	f.17.2 — Cytochrome c oxidase subunit II-like, transmembrane region
Family Family family	f.17.2.1 — Cytochrome c oxidase subunit II-like, transmembrane region

Domain ID domain_id	d6wtib2
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

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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	2.38 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	334222

The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli

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

Cytochrome o ubiquinol oxidase, subunit I

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 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

Cytochrome o 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 o ubiquinol oxidase, 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

6wti__assembly_1__model_1

6wti__assembly_1__model_1 | I(q)

6wti__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 (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 polymer

Polymer Polymer

Source Source

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) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)