8QZQ | pdb_00008qzq

Single particle cryo-EM co-structure of E. coli AcrB with bound BDM91531 inhibitor

PDB DOI: https://doi.org/10.2210/pdb8QZQ/pdb
EM Map EMD-18780: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2023-10-29 Released: 2024-11-06
Deposition Author(s): Boernsen, C., Mueller, R.T., Pos, K.M., Frangakis, A.S.
Funding Organization(s): German Federal Ministry for Education and Research, Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.23 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8QZQ

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

Literature

Single particle cryo-EM co-structure of E. coli AcrB with bound BDM91531 inhibitor at 3.23 A resolution

Boernsen, C., Mueller, R.T.

To be published.

Macromolecule Content

Total Structure Weight: 342.1 kDa
Atom Count: 23,579
Modeled Residue Count: 3,093
Deposited Residue Count: 3,147
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux pump subunit AcrB	A, B, C	1,049	Escherichia coli K-12	Mutation(s): 0 Gene Names: acrB Membrane Entity: Yes
UniProt
Find proteins for P31224 (Escherichia coli (strain K12)) Explore P31224 Go to UniProtKB: P31224
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31224
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WR6 Query on WR6 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	[(2~{R})-1-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-3-undecanoyloxy-propan-2-yl] tricosanoate C₄₀ H₇₉ O₁₀ P QVTMHGKJALUQCM-XPSQVAKYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
XE9 (Subject of Investigation/LOI) Query on XE9 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	[3-(3-chloranyl-2-piperazin-1-yl-quinolin-6-yl)phenyl]methanamine C₂₀ H₂₁ Cl N₄ PMBAQAZUQBDHLD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.23 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-11-06

Deposition Author(s):

Frangakis, A.S.

Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	BMBF- 16GW0236K
Agence Nationale de la Recherche (ANR)	France	ANR-19-AMRB-0007

Revision History (Full details and data files)

Version 1.0: 2024-11-06
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.