4DX5

Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop.

Eicher, T.Cha, H.J.Seeger, M.A.Brandstatter, L.El-Delik, J.Bohnert, J.A.Kern, W.V.Verrey, F.Grutter, M.G.Diederichs, K.Pos, K.M.

(2012) Proc Natl Acad Sci U S A 109: 5687-5692

  • DOI: https://doi.org/10.1073/pnas.1114944109
  • Primary Citation of Related Structures:  
    4DX5, 4DX6, 4DX7

  • PubMed Abstract: 

    AcrAB-TolC is the major efflux protein complex in Escherichia coli extruding a vast variety of antimicrobial agents from the cell. The inner membrane component AcrB is a homotrimer, and it has been postulated that the monomers cycle consecutively through three conformational stages designated loose (L), tight (T), and open (O) in a concerted fashion. Binding of drugs has been shown at a periplasmic deep binding pocket in the T conformation. The initial drug-binding step and transport toward this drug-binding site has been elusive thus far. Here we report high resolution structures (1.9-2.25 Å) of AcrB/designed ankyrin repeat protein (DARPin) complexes with bound minocycline or doxorubicin. In the AcrB/doxorubicin cocrystal structure, binding of three doxorubicin molecules is apparent, with one doxorubicin molecule bound in the deep binding pocket of the T monomer and two doxorubicin molecules in a stacked sandwich arrangement in an access pocket at the lateral periplasmic cleft of the L monomer. This access pocket is separated from the deep binding pocket apparent in the T monomer by a switch-loop. The localization and conformational flexibility of this loop seems to be important for large substrates, because a G616N AcrB variant deficient in macrolide transport exhibits an altered conformation within this loop region. Transport seems to be a stepwise process of initial drug uptake in the access pocket of the L monomer and subsequent accommodation of the drug in the deep binding pocket during the L to T transition to the internal deep binding pocket of the T monomer.


  • Organizational Affiliation

    Institute of Biochemistry and Cluster of Excellence Frankfurt-Macromolecular Complexes, Goethe-University Frankfurt, D-60438 Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acriflavine resistance protein B
A, B, C
1,057Escherichia 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DARPIN
D, E
169synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMU
Query on LMU

Download Ideal Coordinates CCD File 
DA [auth B]DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
LMT
Query on LMT

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AA [auth B]
G [auth A]
H [auth A]
I [auth A]
IA [auth C]
AA [auth B],
G [auth A],
H [auth A],
I [auth A],
IA [auth C],
N [auth A],
T [auth B],
Z [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
MIY
Query on MIY

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S [auth B](4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE
C23 H27 N3 O7
DYKFCLLONBREIL-KVUCHLLUSA-N
C14
Query on C14

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Y [auth B]TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
D12
Query on D12

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KA [auth C],
OA [auth C],
P [auth A],
V [auth B]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
UND
Query on UND

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ZA [auth C]UNDECANE
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
D10
Query on D10

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AB [auth C]
L [auth A]
NA [auth C]
PA [auth C]
U [auth B]
AB [auth C],
L [auth A],
NA [auth C],
PA [auth C],
U [auth B],
W [auth B]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
DD9
Query on DD9

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RA [auth C]nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
OCT
Query on OCT

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J [auth A]
JA [auth C]
K [auth A]
LA [auth C]
MA [auth C]
J [auth A],
JA [auth C],
K [auth A],
LA [auth C],
MA [auth C],
SA [auth C],
WA [auth C]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
SO4
Query on SO4

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YA [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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BB [auth D]
CA [auth B]
CB [auth D]
DB [auth E]
EA [auth B]
BB [auth D],
CA [auth B],
CB [auth D],
DB [auth E],
EA [auth B],
F [auth A],
FA [auth B],
GA [auth B],
HA [auth C],
O [auth A],
Q [auth B],
R [auth B],
UA [auth C],
VA [auth C],
XA [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
HEX
Query on HEX

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BA [auth B],
M [auth A],
QA [auth C],
TA [auth C],
X [auth B]
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.99α = 90
b = 161.72β = 90
c = 245.97γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2014-01-29
    Changes: Source and taxonomy
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Structure summary