6Q4P

Fusidic acid bound AcrB_N298A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Binding and Transport of Carboxylated Drugs by the Multidrug Transporter AcrB.

Tam, H.K.Malviya, V.N.Foong, W.E.Herrmann, A.Malloci, G.Ruggerone, P.Vargiu, A.V.Pos, K.M.

(2020) J Mol Biol 432: 861-877

  • DOI: 10.1016/j.jmb.2019.12.025
  • Primary Citation of Related Structures:  
    6Q4N, 6Q4P, 6Q4O

  • PubMed Abstract: 
  • AcrAB(Z)-TolC is the main drug efflux transporter complex in Escherichia coli. The extrusion of various toxic compounds depends on several drug binding sites within the trimeric AcrB transporter. Membrane-localized carboxylated substrates, such as fusidic acid and hydrophobic β-lactams, access the pump via a groove between the transmembrane helices TM1 and TM2 ...

    AcrAB(Z)-TolC is the main drug efflux transporter complex in Escherichia coli. The extrusion of various toxic compounds depends on several drug binding sites within the trimeric AcrB transporter. Membrane-localized carboxylated substrates, such as fusidic acid and hydrophobic β-lactams, access the pump via a groove between the transmembrane helices TM1 and TM2. In this article, the transport route from the initial TM1/TM2 groove binding site toward the deep binding pocket located in the periplasmic part has been addressed via molecular modeling studies followed by functional and structural characterization of several AcrB variants. We propose that membrane-embedded drugs bind initially to the TM1/TM2 groove, are oriented by the AcrB PN2 subdomain, and are subsequently transported via a PN2/PC1 interface pathway directly toward the deep binding pocket. Our work emphasizes the exploitation of multiple transport pathways by AcrB tuned to substrate physicochemical properties related to the polyspecificity of the pump.


    Related Citations: 
    • Fusidic acid bound AcrB_N298A
      Tam, H.K., Pos, K.M.
      () To be published --: --

    Organizational Affiliation

    Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt Am Main, Germany. Electronic address: pos@em.uni-frankfurt.de.



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): 1 
Gene Names: acrBacrEb0462JW0451
Membrane Entity: Yes 
UniProt
Find proteins for P31224 (Escherichia coli (strain K12))
Explore P31224 
Go to UniProtKB:  P31224
Protein Feature View
Expand
  • 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 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PTY
Query on PTY

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

Download Ideal Coordinates CCD File 
S [auth B]FUSIDIC ACID
C31 H48 O6
IECPWNUMDGFDKC-MZJAQBGESA-N
 Ligand Interaction
LMT
Query on LMT

Download Ideal Coordinates CCD File 
F [auth A] , FA [auth C] , G [auth A] , GA [auth C] , H [auth A] , HA [auth C] , I [auth A] , P [auth B] , 
F [auth A],  FA [auth C],  G [auth A],  GA [auth C],  H [auth A],  HA [auth C],  I [auth A],  P [auth B],  Q [auth B],  R [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
DDR
Query on DDR

Download Ideal Coordinates CCD File 
V [auth B](2S)-3-hydroxypropane-1,2-diyl didecanoate
C23 H44 O5
GNSDEDOVXZDMKM-NRFANRHFSA-N
 Ligand Interaction
ETE
Query on ETE

Download Ideal Coordinates CCD File 
UA [auth C]2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C9 H20 O5
ZNYRFEPBTVGZDN-UHFFFAOYSA-N
 Ligand Interaction
DDQ
Query on DDQ

Download Ideal Coordinates CCD File 
K [auth A], LA [auth C], MA [auth C], NA [auth C], W [auth B], X [auth B]DECYLAMINE-N,N-DIMETHYL-N-OXIDE
C12 H27 N O
ZRKZFNZPJKEWPC-UHFFFAOYSA-N
 Ligand Interaction
C14
Query on C14

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KA [auth C]TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
 Ligand Interaction
D12
Query on D12

Download Ideal Coordinates CCD File 
J [auth A], JA [auth C], U [auth B]DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
 Ligand Interaction
D10
Query on D10

Download Ideal Coordinates CCD File 
EA [auth B]DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
 Ligand Interaction
OCT
Query on OCT

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

Download Ideal Coordinates CCD File 
BA [auth B], CA [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
DA [auth B], L [auth A], M [auth A], N [auth A], TA [auth C], WA [auth E]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HEX
Query on HEX

Download Ideal Coordinates CCD File 
O [auth A], VA [auth C]HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth B], PA [auth C], QA [auth C], RA [auth C], SA [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.222α = 90
b = 162.632β = 90
c = 245.467γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-12-06 
  • Released Date: 2019-11-13 
  • Deposition Author(s): Tam, H.K., Pos, K.M.

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: 2019-11-13
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references