7n9z

E. coli cytochrome bo3 in MSP nanodisc

Method: ELECTRON MICROSCOPY

▼

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

Cytochrome o ubiquinol oxidase, subunit I

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	Ubiquinol oxidase subunit 2 × 1 （A0A024L5V9） Cytochrome o ubiquinol oxidase × 1 （D6I7E4） Cytochrome o ubiquinol oxidase, subunit IV × 1 （I2RK84） Ubiquinone-8 × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 9 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2 HEME O × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 CARDIOLIPIN × 1 COPPER (II) ION × 1 ZINC ION × 1 water × 4	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 F； PDBConstruct 1–663； UniProt 1–663

Ubiquinol oxidase subunit 2

OrganismNot specified

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） Ubiquinone-8 × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 9 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2 HEME O × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 CARDIOLIPIN × 1 COPPER (II) ION × 1 ZINC ION × 1 water × 4	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 G； PDBConstruct 1–315； UniProt 1–315

Cytochrome o ubiquinol oxidase

OrganismNot specified

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） Ubiquinone-8 × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 9 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2 HEME O × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 CARDIOLIPIN × 1 COPPER (II) ION × 1 ZINC ION × 1 water × 4	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 H； PDBConstruct 1–204； UniProt 1–204

Cytochrome o ubiquinol oxidase, subunit IV

OrganismNot specified

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） Ubiquinone-8 × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 9 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2 HEME O × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 CARDIOLIPIN × 1 COPPER (II) ION × 1 ZINC ION × 1 water × 4	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 I； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7n9z
Deposition date deposition_date	2021-06-19
Structure title title	E. coli cytochrome bo3 in MSP nanodisc
Keywords keywords	Ubiquinone, Heme-copper Oxidoreductase, Electron transport, Bioenergetics, Proton pump, Membrane protein; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

7n9z__assembly_1__model_1

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

Download this curve (.dat)

7n9z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7n9z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.43 Å
Rg (electron density)	30.91 Å
Total Rg	31.72 Å
Atom count	20611
Residues	1202
Excluded volume	188710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7n9z__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (13)

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	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F
Atom count atom_count	20938

MFGKLSLDAVPFHEPIVMVTIAGIILGGLALVGLITYFGKWTYLWKEWLTSVDHKRLGIMYIIVAIVMLLRGFADAIMMRSQQALASAGEAGFLPPHHYDQIFTAHGVIMIFFVAMPFVIGLMNLVVPLQIGARDVAFPFLNNLSFWFTVVGVILVNVSLGVGEFAQTGWLAYPPLSGIEYSPGVGVDYWIWSLQLSGIGTTLTGINFFVTILKMRAPGMTMFKMPVFTWASLCANVLIIASFPILTVTVALLTLDRYLGTHFFTNDMGGNMMMYINLIWAWGHPEVYILILPVFGVFSEIAATFSRKRLFGYTSLVWATVCITVLSFIVWLHHFFTMGAGANVNAFFGITTMIIAIPTGVKIFNWLFTMYQGRIVFHSAMLWTIGFIVTFSVGGMTGVLLAVPGADFVLHNSLFLIAHFHNVIIGGVVFGCFAGMTYWWPKAFGFKLNETWGKRAFWFWIIGFFVAFMPLYALGFMGMTRRLSQQIDPQFHTMLMIAASGAVLIALGILCLVIQMYVSIRDRDQNRDLTGDPWGGRTLEWATSSPPPFYNFAVVPHVHERDAFWEMKEKGEAYKKPDHYEEIHMPKNSGAGIVIAAFSTIFGFAMIWHIWWLAIVGFAGMIITWIVKSFDEDVDYYVPVAEIEKLENQHFDEITKAGLKNGN

Entity 2 Entity 2 polymer

Description description	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	G

MRLRKYNKSLGWLSLFAGTVLLSGCNSALLDPKGQIGLEQRSLILTAFGLMLIVVIPAILMAVGFAWKYRASNKDAKYSPNWSHSNKVEAVVWTVPILIIIFLAVLTWKTTHALEPSKPLAHDEKPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANTPVYFKVTSNSVMNSFFIPRLGSQIYAMAGMQTRLHLIANEPGTYDGISASYSGPGFSGMKFKAIATPDRAAFDQWVAKAKQSPNTMSDMAAFEKLAAPSEYNQVEYFSNVKPDLFADVINKFMAHGKSMDMTQPEGEHSAHEGMEGMDMSHAESAH

Entity 3 Entity 3 polymer

Description description	Cytochrome o 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	H

MATDTLTHATAHAHEHGHHDAGGTKIFGFWIYLMSDCILFSILFATYAVLVNGTAGGPTGKDIFELPFVLVETFLLLFSSITYGMAAIAMYKNNKSQVISWLALTWLFGAGFIGMEIYEFHHLIVNGMGPDRSGFLSAFFALVGTHGLHVTSGLIWMAVLMVQIARRGLTSTNRTRIMCLSLFWHFLDVVWICVFTVVYLMGAM

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	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MSHSTDHSGASHGSVKTYMTGFILSIILTVIPFWMVMTGAASPAVILGTILAMAVVQVLVHLVCFLHMNTKSDEGWNMTAFVFTVLIIAILVVGSIWIMWNLNYNMMMH

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
Molecular weight formula_weight	723.0 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 7 Entity 7 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

Entity 8 Entity 8 non-polymer

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

Entity 9 Entity 9 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 10 Entity 10 non-polymer

Description description	CARDIOLIPIN
Molecular weight formula_weight	1464.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 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 12 Entity 12 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 13 Entity 13 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	250

▶

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	2.190 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.19 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	94681

E. coli cytochrome bo3 in MSP nanodisc

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

7n9z__assembly_1__model_1

7n9z__assembly_1__model_1 | I(q)

7n9z__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (13)

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

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 water

7. Citations (1)