5JMN

Fusidic acid bound AcrB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Transport of lipophilic carboxylates is mediated by transmembrane helix 2 in multidrug transporter AcrB.

Oswald, C.Tam, H.K.Pos, K.M.

(2016) Nat Commun 7: 13819-13819

  • DOI: 10.1038/ncomms13819
  • Primary Citation of Related Structures:  
    5JMN

  • PubMed Abstract: 
  • The deployment of multidrug efflux pumps is a powerful defence mechanism for Gram-negative bacterial cells when exposed to antimicrobial agents. The major multidrug efflux transport system in Escherichia coli, AcrAB-TolC, is a tripartite system using the proton-motive force as an energy source ...

    The deployment of multidrug efflux pumps is a powerful defence mechanism for Gram-negative bacterial cells when exposed to antimicrobial agents. The major multidrug efflux transport system in Escherichia coli, AcrAB-TolC, is a tripartite system using the proton-motive force as an energy source. The polyspecific substrate-binding module AcrB uses various pathways to sequester drugs from the periplasm and outer leaflet of the inner membrane. Here we report the asymmetric AcrB structure in complex with fusidic acid at a resolution of 2.5 Å and mutational analysis of the putative fusidic acid binding site at the transmembrane domain. A groove shaped by the interface between transmembrane helix 1 (TM1) and TM2 specifically binds fusidic acid and other lipophilic carboxylated drugs. We propose that these bound drugs are actively displaced by an upward movement of TM2 towards the AcrB periplasmic porter domain in response to protonation events in the transmembrane domain.


    Organizational Affiliation

    Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Multidrug efflux pump subunit AcrBA, B, C1057Escherichia 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, E169synthetic constructMutation(s): 0 
Gene Names: Artificial gene
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PTY
Query on PTY

Download Ideal Coordinates CCD File 
IA [auth C], JA [auth C], KA [auth C], U [auth B]PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
 Ligand Interaction
FUA
Query on FUA

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AA [auth C], F [auth A], O [auth B]FUSIDIC ACID
C31 H48 O6
IECPWNUMDGFDKC-MZJAQBGESA-N
 Ligand Interaction
LMT
Query on LMT

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BA [auth C] , CA [auth C] , DA [auth C] , EA [auth C] , G [auth A] , H [auth A] , I [auth A] , P [auth B] , 
BA [auth C],  CA [auth C],  DA [auth C],  EA [auth C],  G [auth A],  H [auth A],  I [auth A],  P [auth B],  Q [auth B],  R [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
P3G
Query on P3G

Download Ideal Coordinates CCD File 
X [auth B]3,6,9,12,15-PENTAOXAHEPTADECANE
C12 H26 O5
HYDWALOBQJFOMS-UHFFFAOYSA-N
 Ligand Interaction
ETE
Query on ETE

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L [auth A], M [auth A], OA [auth C]2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C9 H20 O5
ZNYRFEPBTVGZDN-UHFFFAOYSA-N
 Ligand Interaction
D12
Query on D12

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LA [auth C], MA [auth C], NA [auth C], V [auth B]DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
 Ligand Interaction
D10
Query on D10

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Y [auth B], Z [auth B]DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
 Ligand Interaction
OCT
Query on OCT

Download Ideal Coordinates CCD File 
PA [auth C], W [auth B]N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
FA [auth C], J [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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GA [auth C], HA [auth C], K [auth A], RA [auth D], S [auth B], SA [auth E], T [auth B], TA [auth E]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HEX
Query on HEX

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.654α = 90
b = 163.248β = 90
c = 246.042γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB807 (Transport and Communication across Biological Membranes
German Research FoundationGermanyDFG EXC115 (Cluster of Excellence Frankfurt Macromolecular Complexes)

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references
  • Version 1.2: 2017-01-11
    Changes: Database references