5NC5

Crystal structure of AcrBZ in complex with antibiotic puromycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An allosteric transport mechanism for the AcrAB-TolC Multidrug Efflux Pump.

Wang, Z.Fan, G.Hryc, C.F.Blaza, J.N.Serysheva, I.I.Schmid, M.F.Chiu, W.Luisi, B.F.Du, D.

(2017) Elife 6: --

  • DOI: 10.7554/eLife.24905
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial efflux pumps confer multidrug resistance by transporting diverse antibiotics from the cell. In Gram-negative bacteria, some of these pumps form multi-protein assemblies that span the cell envelope. Here, we report the near-atomic resolution ...

    Bacterial efflux pumps confer multidrug resistance by transporting diverse antibiotics from the cell. In Gram-negative bacteria, some of these pumps form multi-protein assemblies that span the cell envelope. Here, we report the near-atomic resolution cryoEM structures of the Escherichia coli AcrAB-TolC multidrug efflux pump in resting and drug transport states, revealing a quaternary structural switch that allosterically couples and synchronizes initial ligand binding with channel opening. Within the transport-activated state, the channel remains open even though the pump cycles through three distinct conformations. Collectively, our data provide a dynamic mechanism for the assembly and operation of the AcrAB-TolC pump.


    Organizational Affiliation

    National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Multidrug efflux pump subunit AcrB
A, B, C
1049Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: acrB (acrE)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Multi-Drug Efflux Transporters
Protein: 
AcrB bacterial multi-drug efflux transporter
Find proteins for P31224 (Escherichia coli (strain K12))
Go to UniProtKB:  P31224
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DARPin
D, E
169N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Multidrug efflux pump accessory protein AcrZ
F, G, H
49Escherichia coli O157:H7Mutation(s): 0 
Gene Names: acrZ
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Multi-Drug Efflux Transporters
Protein: 
AcrB bacterial multi-drug efflux transporter
Find proteins for P0AAX1 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AAX1
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PUY
Query on PUY

Download SDF File 
Download CCD File 
B
PUROMYCIN
C22 H29 N7 O5
RXWNCPJZOCPEPQ-NVWDDTSBSA-N
 Ligand Interaction
D12
Query on D12

Download SDF File 
Download CCD File 
A, B, C
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
 Ligand Interaction
LMT
Query on LMT

Download SDF File 
Download CCD File 
A
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
D10
Query on D10

Download SDF File 
Download CCD File 
A, B, C
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
 Ligand Interaction
DD9
Query on DD9

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Download CCD File 
A, B, C
nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
 Ligand Interaction
HEX
Query on HEX

Download SDF File 
Download CCD File 
C
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 147.245α = 90.00
b = 167.646β = 90.00
c = 249.980γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
iMOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-03-03 
  • Released Date: 2017-04-12 
  • Deposition Author(s): Du, D., Luisi, B.

Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomRG61065

Revision History 

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-04-19
    Type: Atomic model