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


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.7554/eLife.24905
  • Primary Citation of Related Structures:  
    5NC5, 5NG5, 5O66, 5V5S

  • 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. 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multidrug efflux pump subunit AcrB
A, B, C
1,049Escherichia 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31224
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DARPin
D, E
169Escherichia coliMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Multidrug efflux pump accessory protein AcrZ
F, G, H
49Escherichia 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AAX1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / 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
PUY
Query on PUY

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

Download Ideal Coordinates CCD File 
K [auth A]
QA [auth B]
T [auth A]
UA [auth C]
XA [auth C]
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
D10
Query on D10

Download Ideal Coordinates CCD File 
AA [auth B]
CB [auth C]
DA [auth B]
DB [auth C]
EB [auth C]
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
DD9
Query on DD9

Download Ideal Coordinates CCD File 
AB [auth C]
BA [auth B]
BB [auth C]
CA [auth B]
EA [auth B]
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
HEX
Query on HEX

Download Ideal Coordinates CCD File 
WA [auth C]HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
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

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description