7OSE | pdb_00007ose

cytochrome bd-II type oxidase with bound aurachin D

PDB DOI: https://doi.org/10.2210/pdb7OSE/pdb
EM Map EMD-13048: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli BW25113
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2021-06-08 Released: 2021-11-17
Deposition Author(s): Grauel, A., Kaegi, J., Rasmussen, T., Wohlwend, D., Boettcher, B., Friedrich, T.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of Escherichia coli cytochrome bd-II type oxidase with bound aurachin D.

Grauel, A., Kagi, J., Rasmussen, T., Makarchuk, I., Oppermann, S., Moumbock, A.F.A., Wohlwend, D., Muller, R., Melin, F., Gunther, S., Hellwig, P., Bottcher, B., Friedrich, T.

(2021) Nat Commun 12: 6498-6498

PubMed: 34764272 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-26835-2
Primary Citation Related Structures:
7OSE

PubMed Abstract:
Cytochrome bd quinol:O ₂ oxidoreductases are respiratory terminal oxidases so far only identified in prokaryotes, including several pathogenic bacteria. Escherichia coli contains two bd oxidases of which only the bd-I type is structurally characterized. Here, we report the structure of the Escherichia coli cytochrome bd-II type oxidase with the bound inhibitor aurachin D as obtained by electron cryo-microscopy at 3 Å resolution. The oxidase consists of subunits AppB, C and X that show an architecture similar to that of bd-I. The three heme cofactors are found in AppC, while AppB is stabilized by a structural ubiquinone-8 at the homologous positions. A fourth subunit present in bd-I is lacking in bd-II. Accordingly, heme b ₅₉₅ is exposed to the membrane but heme d embedded within the protein and showing an unexpectedly high redox potential is the catalytically active centre. The structure of the Q-loop is fully resolved, revealing the specific aurachin binding.

Organizational Affiliation

Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.

Macromolecule Content

Total Structure Weight: 213.94 kDa
Atom Count: 14,882
Modeled Residue Count: 1,816
Deposited Residue Count: 1,844
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome bd-II ubiquinol oxidase subunit 1	A, D	514	Escherichia coli BW25113	Mutation(s): 0 EC: 7.1.1.3 Membrane Entity: Yes
UniProt
Find proteins for P26459 (Escherichia coli (strain K12)) Explore P26459 Go to UniProtKB: P26459
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26459
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome bd-II ubiquinol oxidase subunit 2	B, E	378	Escherichia coli BW25113	Mutation(s): 0 Gene Names: appB, cbdB, cyxB, b0979, JW0961 EC: 7.1.1.3 Membrane Entity: Yes
UniProt
Find proteins for P26458 (Escherichia coli (strain K12)) Explore P26458 Go to UniProtKB: P26458
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26458
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cytochrome bd-II ubiquinol oxidase subunit AppX	C, F	30	Escherichia coli BW25113	Mutation(s): 0 Gene Names: appX, yccB, b4592, JW0961.1, b0979.1 Membrane Entity: Yes
UniProt
Find proteins for P24244 (Escherichia coli (strain K12)) Explore P24244 Go to UniProtKB: P24244
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24244
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UQ8 Query on UQ8 Download:Ideal Coordinates CCD File SDF format, chain P [auth E] SDF format, chain K [auth B] MOL2 format, chain P [auth E] MOL2 format, chain K [auth B] mmCIF format, chain P [auth E] mmCIF format, chain K [auth B]	K [auth B], P [auth E]	Ubiquinone-8 C₄₉ H₇₄ O₄ ICFIZJQGJAJRSU-SGHXUWJISA-N		Interactions Focus chain K [auth B] Focus chain P [auth E] Interactions & Density Focus chain K [auth B] Focus chain P [auth E]
HDD Query on HDD Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain I [auth A] MOL2 format, chain N [auth D] MOL2 format, chain I [auth A] mmCIF format, chain N [auth D] mmCIF format, chain I [auth A]	I [auth A], N [auth D]	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE C₃₄ H₃₂ Fe N₄ O₅ UMGOPAWIGKFTRK-QQDQPIDJSA-N		Interactions Focus chain I [auth A] Focus chain N [auth D] Interactions & Density Focus chain I [auth A] Focus chain N [auth D]
HEB Query on HEB Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain L [auth D] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], L [auth D], M [auth D]	HEME B/C C₃₄ H₃₄ Fe N₄ O₄ NEGHHAJBRZGUAY-RGGAHWMASA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth D] Focus chain M [auth D]
0NI Query on 0NI Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain J [auth A] MOL2 format, chain O [auth D] MOL2 format, chain J [auth A] mmCIF format, chain O [auth D] mmCIF format, chain J [auth A]	J [auth A], O [auth D]	Aurachin D C₂₅ H₃₃ N O JHMLNOXMSHURLQ-LULTWYLNSA-N		Interactions Focus chain J [auth A] Focus chain O [auth D] Interactions & Density Focus chain J [auth A] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	19-4092

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-11-17

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	278002225/RTG 2202

Revision History (Full details and data files)

Version 1.0: 2021-11-17
Type: Initial release
Version 1.1: 2021-11-24
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Refinement description, Source and taxonomy, Structure summary