8GO3

Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent

PDB DOI: https://doi.org/10.2210/pdb8GO3/pdb
EM Map EMD-34171: EMDB EMDataResource

Classification: TRANSLOCASE
Organism(s): Escherichia coli K-12
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2022-08-24 Released: 2023-08-30
Deposition Author(s): Cao, H.Y., Li, K., Li, C.Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.09 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent

Cao, H.Y., Li, K., Li, C.Y.

To be published.

Macromolecule Content

Total Structure Weight: 147.79 kDa
Atom Count: 9,739
Modelled Residue Count: 1,203
Deposited Residue Count: 1,291
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome bo(3) ubiquinol oxidase subunit 1	A	663	Escherichia coli K-12	Mutation(s): 0 EC: 7.1.1.3 Membrane Entity: Yes
UniProt
Find proteins for P0ABI8 (Escherichia coli (strain K12)) Explore P0ABI8 Go to UniProtKB: P0ABI8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ABI8
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome bo(3) ubiquinol oxidase subunit 2	B	315	Escherichia coli K-12	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0ABJ1 (Escherichia coli (strain K12)) Explore P0ABJ1 Go to UniProtKB: P0ABJ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ABJ1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ubiquinol oxidase	C	204	Escherichia coli K-12	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0ABJ3 (Escherichia coli (strain K12)) Explore P0ABJ3 Go to UniProtKB: P0ABJ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ABJ3
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome bo(3) ubiquinol oxidase subunit 4	D	109	Escherichia coli K-12	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0ABJ6 (Escherichia coli (strain K12)) Explore P0ABJ6 Go to UniProtKB: P0ABJ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ABJ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEO Query on HEO Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	HEME O C₄₉ H₅₈ Fe N₄ O₅ FRKORVCRVCLRBA-BZKSIRDQSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
3PE Query on 3PE Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth C]	I [auth A], J [auth C]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain I [auth A] Focus chain J [auth C] Interactions & Density Focus chain I [auth A] Focus chain J [auth C]
UQ8 Query on UQ8 Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	Ubiquinone-8 C₄₉ H₇₄ O₄ ICFIZJQGJAJRSU-SGHXUWJISA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]