8QZL | pdb_00008qzl

Single particle cryo-EM co-structure of Klebsiella pneumoniae AcrB with the BDM91288 efflux pump inhibitor at 3.42 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb8QZL/pdb
EM Map EMD-18777: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Klebsiella pneumoniae subsp. pneumoniae DSM 30104 = JCM 1662 = NBRC 14940
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2023-10-27 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: 3.42 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8QZL

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

Literature

Single particle cryo-EM co-structure of Klebsiella pneumoniae AcrB with the BDM91288 efflux pump inhibitor at 3.42 Angstrom resolution

Boernsen, C., Mueller, R.T.

To be published.

Macromolecule Content

Total Structure Weight: 344.14 kDa
Atom Count: 23,364
Modeled Residue Count: 3,069
Deposited Residue Count: 3,168
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Efflux pump membrane transporter	A, B, C	1,056	Klebsiella pneumoniae subsp. pneumoniae DSM 30104 = JCM 1662 = NBRC 14940	Mutation(s): 0 Gene Names: UUU_08720 Membrane Entity: Yes
UniProt
Find proteins for W1DJX9 (Klebsiella pneumoniae IS43) Explore W1DJX9 Go to UniProtKB: W1DJX9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W1DJX9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WQW (Subject of Investigation/LOI) Query on WQW Download:Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain D [auth A] MOL2 format, chain E [auth C] MOL2 format, chain D [auth A] mmCIF format, chain E [auth C] mmCIF format, chain D [auth A]	D [auth A], E [auth C]	3-chloranyl-2,6-di(piperazin-4-ium-1-yl)quinoline C₁₇ H₂₄ Cl N₅ WOZFYSNOHHYUAU-UHFFFAOYSA-P		Interactions Focus chain D [auth A] Focus chain E [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.42 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4

Structure Validation

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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.