2RDD | pdb_00002rdd

X-ray crystal structure of AcrB in complex with a novel transmembrane helix.

PDB DOI: https://doi.org/10.2210/pdb2RDD/pdb

Classification: Membrane protein/TRANSPORT PROTEIN
Organism(s): Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2007-09-22 Released: 2007-12-11
Deposition Author(s): Tornroth-Horsefield, S., Gourdon, P., Horsefield, R., Neutze, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.317 (Depositor), 0.325 (DCC)
R-Value Work:
0.279 (Depositor), 0.286 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of AcrB in complex with a single transmembrane subunit reveals another twist.

Tornroth-Horsefield, S., Gourdon, P., Horsefield, R., Brive, L., Yamamoto, N., Mori, H., Snijder, A., Neutze, R.

(2007) Structure 15: 1663-1673

PubMed: 18073115 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2007.09.023
Primary Citation Related Structures:
2RDD

PubMed Abstract:
Bacterial drug resistance is a serious concern for human health. Multidrug efflux pumps export a broad variety of substrates out of the cell and thereby convey resistance to the host. In Escherichia coli, the AcrB:AcrA:TolC efflux complex forms a principal transporter for which structures of the individual component proteins have been determined in isolation. Here, we present the X-ray structure of AcrB in complex with a single transmembrane protein, assigned by mass spectrometry as YajC. A specific rotation of the periplasmic porter domain of AcrB is also revealed, consistent with the hypothesized "twist-to-open" mechanism for TolC activation. Growth experiments with yajc-deleted E. coli reveal a modest increase in the organism's susceptibility to beta-lactam antibiotics, but this effect could not conclusively be attributed to the loss of interactions between YajC and AcrB.

Organizational Affiliation

Department of Chemistry, Biochemistry and Biophysics, Gothenburg University, 40530 Gothenburg, Sweden. susanna.tornroth@chem.gu.se

Macromolecule Content

Total Structure Weight: 118.81 kDa
Atom Count: 8,026
Modeled Residue Count: 1,055
Deposited Residue Count: 1,086
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acriflavine resistance protein B	A	1,049	Escherichia coli	Mutation(s): 0 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

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0092 membrane protein yajC	B	37	Escherichia coli	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0ADZ7 (Escherichia coli (strain K12)) Explore P0ADZ7 Go to UniProtKB: P0ADZ7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ADZ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AIC Query on AIC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	(2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID C₁₆ H₁₉ N₃ O₄ S AVKUERGKIZMTKX-NJBDSQKTSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.317 (Depositor), 0.325 (DCC)
R-Value Work: 0.279 (Depositor), 0.286 (DCC)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.097	α = 90
b = 145.097	β = 90
c = 511.644	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-12-11

Deposition Author(s):

Tornroth-Horsefield, S.

Gourdon, P.

Horsefield, R.

Neutze, R.

Revision History (Full details and data files)

Version 1.0: 2007-12-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description