9ufv

Ubiquinol Binding Site of Cytochrome bo3 from Acinetobacter baumannii

Method: ELECTRON MICROSCOPY

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

Cytochrome bo(3) ubiquinol oxidase subunit 1

Acinetobacter baumannii

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 （A0A0D5YHQ6） Cytochrome bo(3) ubiquinol oxidase subunit 3 × 1 （V5VBX7） Cytochrome bo(3) ubiquinol oxidase subunit 4 × 1 （V5VBE6） PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1 COPPER (II) ION × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 Ubiquinone-8 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0AB73F7N6_ACIBA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–660； UniProt 4–663

Ubiquinol oxidase subunit 2

Acinetobacter baumannii

UniProt A0A0D5YHQ6

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 （A0AB73F7N6） Cytochrome bo(3) ubiquinol oxidase subunit 3 × 1 （V5VBX7） Cytochrome bo(3) ubiquinol oxidase subunit 4 × 1 （V5VBE6） PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1 COPPER (II) ION × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 Ubiquinone-8 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0D5YHQ6_ACIBA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–277； UniProt 23–299

Cytochrome bo(3) ubiquinol oxidase subunit 3

Acinetobacter baumannii

UniProt V5VBX7

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 （A0AB73F7N6） Ubiquinol oxidase subunit 2 × 1 （A0A0D5YHQ6） Cytochrome bo(3) ubiquinol oxidase subunit 4 × 1 （V5VBE6） PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1 COPPER (II) ION × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 Ubiquinone-8 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	V5VBX7_ACIBA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–191； UniProt 16–206

Cytochrome bo(3) ubiquinol oxidase subunit 4

Acinetobacter baumannii

UniProt V5VBE6

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 （A0AB73F7N6） Ubiquinol oxidase subunit 2 × 1 （A0A0D5YHQ6） Cytochrome bo(3) ubiquinol oxidase subunit 3 × 1 （V5VBX7） PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1 COPPER (II) ION × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 Ubiquinone-8 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	V5VBE6_ACIBA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 9–96； UniProt 22–109

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	9ufv
Deposition date deposition_date	2025-04-10
Structure title title	Ubiquinol Binding Site of Cytochrome bo3 from Acinetobacter baumannii
Keywords keywords	protein pump, ubiquinol, oxidase, 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.

9ufv__assembly_1__model_1

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

Download this curve (.dat)

9ufv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ufv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.37 Å
Rg (electron density)	30.99 Å
Total Rg	31.75 Å
Atom count	10272
Residues	1225
Excluded volume	188940 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ufv__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 bo(3) ubiquinol oxidase subunit 1
Molecular weight formula_weight	74200.3 kDa
EC 编号 ec_number	7.1.1.3
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	10282

IFGKLGWDSIPTEPIVLVTMVFMALGAIAVLGGITYFKKWGYLWKEWFTTVDHKKIGIMYIIVSVVMLLRGFADAIMMRLQLFLAKGGGEGYLHPDHYDQIFTAHGVIMIFFVAMGLVVGMMNISVPLQIGARDVAFPLLNSLSFWLFAGAAGLMMLSLVLGEFAATGWMAYPPLSGIQYSPGVGVDYYIWALQVSGLGTLLSGVNFFVTIIKMRAPGMKLMDMPIFTWTSLCTAVLIIASFPVLTGTLAMLTLDRYFGFHFFTNELGGSPMLYVNLIWTWGHPEVYILVLPAFGLYSEIVATFSRKALFGYKSMVYATIAITVLAFVVWLHHFFTMGAGANVNAFFGIMTMVIAIPTGVKIFSWLFTMYKGRITFTTPMLWTLGFLVTFGIGGLTGVLMAVPPADFLVHNSLFLIAHFHNVIIGGVVFGMFAGIIYYWPKMFGWKLNEAWGKAAFWFWFFGFYFAFMPLYILGFLGMTRRLNTYDNPEWDPYLAIALFGAVLVAIGIACFLMQIIVGFLQRHQNMDYTGDPWDARTLEWATSSPAPFYNFAHEPDASGIDRFWTDKENGVAYARNTKYEDIHMPTDRAAGFVIAMFITLLGFALIWHIWWLVVVSFVAAVVSLIVSSFTKNVDYYVPAAEVERIENERYALLEKHLKKD

Source Source

Source organism organism	Acinetobacter baumannii
NCBI taxonomy ID ncbi_taxonomy_id	470
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquinol oxidase subunit 2
Molecular weight formula_weight	31121.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GDMVLLNSKGPVGQGQSDLMMTAIYLMLLVVIPSIIMALWFGWKYRASNKDADYKPTWAHSTAIEVVVWGIPVIIIGILAWLTWWGSHKYDPYRPLESDKAPLTIQVIAEQFKWIFIYPEQNIATVNEVRFPEKTPLSFKITSNFTMNSFFIPQLGGQIYAMAGMQTHLHLLANETGVYRGFSSNYSGYGFSQMRFKAHSVTEQQFNEWVAAVKAGNGTTINPEAVQKTTLDQAELATLRDGDRSKHQIEHLVNRAKAAGDQEALAKAEAMKPFPTK

Source Source

Source organism organism	Acinetobacter baumannii
NCBI taxonomy ID ncbi_taxonomy_id	470
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Cytochrome bo(3) ubiquinol oxidase subunit 3
Molecular weight formula_weight	21569.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

HEHDDTDLTVFGFWTYLMSDLILFGSLFIAFAVLSSHVPPGTPSAYDLFHESLGYVLTETFALLISSVTFGFAVLASYKKNVNQVITWLFITFLFGATFIGMELYEFHHLVEEGHGPTHSAFLSSFFTLVGTHGIHVTSGLVWMLVLMYQIKTKGLTLPNTRRLACLSLFWHFLDIVWICVFSVVYLLGVL

Source Source

Source organism organism	Acinetobacter baumannii
NCBI taxonomy ID ncbi_taxonomy_id	470
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Cytochrome bo(3) ubiquinol oxidase subunit 4
Molecular weight formula_weight	10882.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GSVKTYMTGFILSIILTVIPFGMVMAGGFSRGLLVTVIAITAVAQVLVQLVYFLHMNTSSEQRWNMIAFIYTILCIAVLLIGSVWIMNYLHYNMMIH

Source Source

Source organism organism	Acinetobacter baumannii
NCBI taxonomy ID ncbi_taxonomy_id	470
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	1,2-Distearoyl-sn-glycerophosphoethanolamine
Molecular weight formula_weight	748.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 9 Entity 9 non-polymer

Description description	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
Molecular weight formula_weight	787.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 10 Entity 10 non-polymer

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

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

Resolution resolution	3.56 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	46373

Ubiquinol Binding Site of Cytochrome bo3 from Acinetobacter baumannii

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

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 bo(3) ubiquinol oxidase subunit 3

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

9ufv__assembly_1__model_1

9ufv__assembly_1__model_1 | I(q)

9ufv__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 (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

7. Citations (1)