9rzv

E. coli cytochrome bd-I dimer bound to menaquinone

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 8	Cytochrome bd-I ubiquinol oxidase subunit 2 × 2 （P0ABK2） Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF) × 2 （A5A618） Cytochrome bd-I ubiquinol oxidase subunit X × 2 （P56100） PROTOPORPHYRIN IX CONTAINING FE × 4 TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE × 2 MENAQUINONE-9 × 4 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE × 6 Ubiquinone-8 × 2 OXYGEN MOLECULE × 2 (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 4 (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 water × 4	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 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 8	Cytochrome bd-I ubiquinol oxidase subunit 1 × 2 （P0ABJ9） Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF) × 2 （A5A618） Cytochrome bd-I ubiquinol oxidase subunit X × 2 （P56100） PROTOPORPHYRIN IX CONTAINING FE × 4 TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE × 2 MENAQUINONE-9 × 4 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE × 6 Ubiquinone-8 × 2 OXYGEN MOLECULE × 2 (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 4 (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 water × 4	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 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 8	Cytochrome bd-I ubiquinol oxidase subunit 1 × 2 （P0ABJ9） Cytochrome bd-I ubiquinol oxidase subunit 2 × 2 （P0ABK2） Cytochrome bd-I ubiquinol oxidase subunit X × 2 （P56100） PROTOPORPHYRIN IX CONTAINING FE × 4 TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE × 2 MENAQUINONE-9 × 4 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE × 6 Ubiquinone-8 × 2 OXYGEN MOLECULE × 2 (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 4 (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 water × 4	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 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 8	Cytochrome bd-I ubiquinol oxidase subunit 1 × 2 （P0ABJ9） Cytochrome bd-I ubiquinol oxidase subunit 2 × 2 （P0ABK2） Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF) × 2 （A5A618） PROTOPORPHYRIN IX CONTAINING FE × 4 TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE × 2 MENAQUINONE-9 × 4 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE × 6 Ubiquinone-8 × 2 OXYGEN MOLECULE × 2 (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 4 (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 water × 4	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 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	9rzv
Deposition date deposition_date	2025-07-16
Structure title title	E. coli cytochrome bd-I dimer bound to menaquinone
Keywords keywords	Oxireductase, Complex, Quinone, Substrate, membrane protein, Escherichia coli, 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.

9rzv__assembly_1__model_1

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

Download this curve (.dat)

9rzv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9rzv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.11 Å
Rg (electron density)	40.27 Å
Total Rg	40.83 Å
Atom count	32830
Residues	1902
Excluded volume	300050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9rzv__assembly_1__model_1`	octameric （8）	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 (13)

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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,a
Atom count atom_count	32907

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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,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	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 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	2

Entity 7 Entity 7 non-polymer

Description description	MENAQUINONE-9
Molecular weight formula_weight	785.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 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	6

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	2

Entity 10 Entity 10 non-polymer

Description description	OXYGEN MOLECULE
Molecular weight formula_weight	32.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

Description description	(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
Molecular weight formula_weight	751.0 kDa
Source method src_method	nat
Copy count entity_count	4

Entity 12 Entity 12 non-polymer

Description description	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
Molecular weight formula_weight	760.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 13 Entity 13 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	77

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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	2.23 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	530094

E. coli cytochrome bd-I dimer bound to menaquinone

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

9rzv__assembly_1__model_1

9rzv__assembly_1__model_1 | I(q)

9rzv__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 (13)

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

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 water

7. Citations (1)