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 

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Ligand Structure Quality Assessment 


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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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Acriflavine resistance protein BA, B, C1,057Escherichia 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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DARPIND, E169synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 12 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
MIY
Query on MIY

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
C14
Query on C14

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Y [auth B]TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
 Ligand Interaction
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
 Ligand Interaction
UND
Query on UND

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ZA [auth C]UNDECANE
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
 Ligand Interaction
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
 Ligand Interaction
DD9
Query on DD9

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RA [auth C]nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
 Ligand Interaction
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
 Ligand Interaction
SO4
Query on SO4

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YA [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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