9se4

E. coli cytochrome bd-I monomer

Method: ELECTRON MICROSCOPY

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

Cytochrome bd-I ubiquinol oxidase subunit 1

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cytochrome bd-I ubiquinol oxidase subunit 2 × 1 （P0ABK2） Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF) × 1 （A5A618） Cytochrome bd-I ubiquinol oxidase subunit X × 1 （P56100） TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE × 1 PROTOPORPHYRIN IX CONTAINING FE × 2 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE × 2 OXYGEN MOLECULE × 1 Ubiquinone-8 × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYDA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–522； UniProt 1–522

Cytochrome bd-I ubiquinol oxidase subunit 2

Escherichia coli K-12

UniProt P0ABK2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cytochrome bd-I ubiquinol oxidase subunit 1 × 1 （P0ABJ9） Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF) × 1 （A5A618） Cytochrome bd-I ubiquinol oxidase subunit X × 1 （P56100） TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE × 1 PROTOPORPHYRIN IX CONTAINING FE × 2 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE × 2 OXYGEN MOLECULE × 1 Ubiquinone-8 × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYDB_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–379； UniProt 1–379

Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF)

Escherichia coli K-12

UniProt A5A618

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cytochrome bd-I ubiquinol oxidase subunit 1 × 1 （P0ABJ9） Cytochrome bd-I ubiquinol oxidase subunit 2 × 1 （P0ABK2） Cytochrome bd-I ubiquinol oxidase subunit X × 1 （P56100） TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE × 1 PROTOPORPHYRIN IX CONTAINING FE × 2 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE × 2 OXYGEN MOLECULE × 1 Ubiquinone-8 × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YNHF_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain H； PDBConstruct 1–29； UniProt 1–29

Cytochrome bd-I ubiquinol oxidase subunit X

Escherichia coli K-12

UniProt P56100

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cytochrome bd-I ubiquinol oxidase subunit 1 × 1 （P0ABJ9） Cytochrome bd-I ubiquinol oxidase subunit 2 × 1 （P0ABK2） Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF) × 1 （A5A618） TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE × 1 PROTOPORPHYRIN IX CONTAINING FE × 2 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE × 2 OXYGEN MOLECULE × 1 Ubiquinone-8 × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYDX_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain X； PDBConstruct 1–37； UniProt 1–37

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	9se4
Deposition date deposition_date	2025-08-15
Structure title title	E. coli cytochrome bd-I monomer
Keywords keywords	Respiration, Complex, Cytochrome, 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.

9se4__assembly_1__model_1

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

Download this curve (.dat)

9se4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9se4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.74 Å
Rg (electron density)	28.43 Å
Total Rg	29.45 Å
Atom count	14601
Residues	894
Excluded volume	133940 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9se4__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 bd-I ubiquinol oxidase subunit 1
Molecular weight formula_weight	58251.7 kDa
EC 编号 ec_number	7.1.1.7
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	14633

MLDIVELSRLQFALTAMYHFLFVPLTLGMAFLLAIMETVYVLSGKQIYKDMTKFWGKLFGINFALGVATGLTMEFQFGTNWSYYSHYVGDIFGAPLAIEGLMAFFLESTFVGLFFFGWDRLGKVQHMCVTWLVALGSNLSALWILVANGWMQNPIASDFNFETMRMEMVSFSELVLNPVAQVKFVHTVASGYVTGAMFILGISAWYMLKGRDFAFAKRSFAIAASFGMAAVLSVIVLGDESGYEMGDVQKTKLAAIEAEWETQPAPAAFTLFGIPDQEEETNKFAIQIPYALGIIATRSVDTPVIGLKELMVQHEERIRNGMKAYSLLEQLRSGSTDQAVRDQFNSMKKDLGYGLLLKRYTPNVADATEAQIQQATKDSIPRVAPLYFAFRIMVACGFLLLAIIALSFWSVIRNRIGEKKWLLRAALYGIPLPWIAVEAGWFVAEYGRQPWAIGEVLPTAVANSSLTAGDLIFSMVLICGLYTLFLVAELFLMFKFARLGPSSLKTGRYHFEQSSTTTQPAR

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Cytochrome bd-I ubiquinol oxidase subunit 2
Molecular weight formula_weight	42479.8 kDa
EC 编号 ec_number	7.1.1.7
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MIDYEVLRFIWWLLVGVLLIGFAVTDGFDMGVGMLTRFLGRNDTERRIMINSIAPHWDGNQVWLITAGGALFAAWPMVYAAAFSGFYVAMILVLASLFFRPVGFDYRSKIEETRWRNMWDWGIFIGSFVPPLVIGVAFGNLLQGVPFNVDEYLRLYYTGNFFQLLNPFGLLAGVVSVGMIITQGATYLQMRTVGELHLRTRATAQVAALVTLVCFALAGVWVMYGIDGYVVKSTMDHYAASNPLNKEVVREAGAWLVNFNNTPILWAIPALGVVLPLLTILTARMDKAAWAFVFSSLTLACIILTAGIAMFPFVMPSSTMMNASLTMWDATSSQLTLNVMTWVAVVLVPIILLYTAWCYWKMFGRITKEDIERNTHSLY

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF)
Molecular weight formula_weight	2999.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MSTDLKFSLVTTIIVLGLIVAVGLTAALH

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Cytochrome bd-I ubiquinol oxidase subunit X
Molecular weight formula_weight	4043.7 kDa
EC 编号 ec_number	7.1.1.7
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

MWYFAWILGTLLACSFGVITALALEHVESGKAGQEDI

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
Molecular weight formula_weight	636.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
Molecular weight formula_weight	648.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	OXYGEN MOLECULE
Molecular weight formula_weight	32.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

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

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	32

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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	2.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	399575

E. coli cytochrome bd-I monomer

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

Cytochrome bd-I 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 bd-I 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 bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF)

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 bd-I ubiquinol oxidase subunit X

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

9se4__assembly_1__model_1

9se4__assembly_1__model_1 | I(q)

9se4__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 water

7. Citations (1)