5NC5

Crystal structure of AcrBZ in complex with antibiotic puromycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    5V5S, 5NG5, 5O66, 5NC5

  • 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 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 ...

    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

    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Multidrug efflux pump subunit AcrBA, B, C1049Escherichia coli K-12Mutation(s): 0 
Gene Names: acrBacrEb0462JW0451
Membrane Entity: Yes 
UniProt
Find proteins for P31224 (Escherichia coli (strain K12))
Explore P31224 
Go to UniProtKB:  P31224
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DARPinD, E169Escherichia coliMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Multidrug efflux pump accessory protein AcrZF, G, H49Escherichia coli O157:H7Mutation(s): 0 
Gene Names: acrZZ0932ECs0790
Membrane Entity: Yes 
UniProt
Find proteins for P0AAX1 (Escherichia coli O157:H7)
Explore P0AAX1 
Go to UniProtKB:  P0AAX1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], S [auth A]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
PUY
Query on PUY

Download Ideal Coordinates CCD File 
PA [auth B]PUROMYCIN
C22 H29 N7 O5
RXWNCPJZOCPEPQ-NVWDDTSBSA-N
 Ligand Interaction
D12
Query on D12

Download Ideal Coordinates CCD File 
K [auth A], QA [auth B], T [auth A], UA [auth C], XA [auth C], YA [auth C], Z [auth B], ZA [auth C]DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
 Ligand Interaction
D10
Query on D10

Download Ideal Coordinates CCD File 
AA [auth B] , CB [auth C] , DA [auth B] , DB [auth C] , EB [auth C] , FA [auth B] , FB [auth C] , GA [auth B] , 
AA [auth B],  CB [auth C],  DA [auth B],  DB [auth C],  EB [auth C],  FA [auth B],  FB [auth C],  GA [auth B],  GB [auth C],  HB [auth C],  IA [auth B],  IB [auth C],  JA [auth B],  L [auth A],  LA [auth B],  M [auth A],  MA [auth B],  N [auth A],  NA [auth B],  P [auth A],  Q [auth A],  RA [auth B],  TA [auth C],  VA [auth C],  W [auth B],  Y [auth B]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
 Ligand Interaction
DD9
Query on DD9

Download Ideal Coordinates CCD File 
AB [auth C] , BA [auth B] , BB [auth C] , CA [auth B] , EA [auth B] , HA [auth B] , KA [auth B] , O [auth A] , 
AB [auth C],  BA [auth B],  BB [auth C],  CA [auth B],  EA [auth B],  HA [auth B],  KA [auth B],  O [auth A],  OA [auth B],  R [auth A],  SA [auth C],  U [auth A],  V [auth A],  X [auth B]
nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
 Ligand Interaction
HEX
Query on HEX

Download Ideal Coordinates CCD File 
WA [auth C]HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.245α = 90
b = 167.646β = 90
c = 249.98γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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  (Full details and data files)

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-04-19
    Changes: Atomic model
  • Version 1.2: 2019-10-16
    Changes: Data collection