6BPP

E. coli MsbA in complex with LPS and inhibitor G092


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural basis for dual-mode inhibition of the ABC transporter MsbA.

Ho, H.Miu, A.Alexander, M.K.Garcia, N.K.Oh, A.Zilberleyb, I.Reichelt, M.Austin, C.D.Tam, C.Shriver, S.Hu, H.Labadie, S.S.Liang, J.Wang, L.Wang, J.Lu, Y.Purkey, H.E.Quinn, J.Franke, Y.Clark, K.Beresini, M.H.Tan, M.W.Sellers, B.D.Maurer, T.Koehler, M.F.T.Wecksler, A.T.Kiefer, J.R.Verma, V.Xu, Y.Nishiyama, M.Payandeh, J.Koth, C.M.

(2018) Nature 557: 196-201

  • DOI: https://doi.org/10.1038/s41586-018-0083-5
  • Primary Citation of Related Structures:  
    6BPL, 6BPP

  • PubMed Abstract: 

    The movement of core-lipopolysaccharide across the inner membrane of Gram-negative bacteria is catalysed by an essential ATP-binding cassette transporter, MsbA. Recent structures of MsbA and related transporters have provided insights into the molecular basis of active lipid transport; however, structural information about their pharmacological modulation remains limited. Here we report the 2.9 Å resolution structure of MsbA in complex with G907, a selective small-molecule antagonist with bactericidal activity, revealing an unprecedented mechanism of ABC transporter inhibition. G907 traps MsbA in an inward-facing, lipopolysaccharide-bound conformation by wedging into an architecturally conserved transmembrane pocket. A second allosteric mechanism of antagonism occurs through structural and functional uncoupling of the nucleotide-binding domains. This study establishes a framework for the selective modulation of ABC transporters and provides rational avenues for the design of new antibiotics and other therapeutics targeting this protein family.


  • Organizational Affiliation

    Structural Biology, Genentech Inc., San Francisco, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipid A export ATP-binding/permease protein MsbA
A, B
582Escherichia coli CFT073Mutation(s): 0 
Gene Names: msbAc1054
EC: 3.6.3 (PDB Primary Data), 7.5.2.6 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q8FJB1 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Explore Q8FJB1 
Go to UniProtKB:  Q8FJB1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8FJB1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-[L-glycero-alpha-D-manno-heptopyranose-(1-7)]L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose
C
10N/A
Glycosylation Resources
GlyTouCan:  G17242FQ
GlyCosmos:  G17242FQ
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
R [auth B]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
R [auth B],
S [auth B],
T [auth B]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
E1M
Query on E1M

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B]
(2E)-3-{6-[(1S)-1-(3-amino-2,6-dichlorophenyl)ethoxy]-4-cyclopropylquinolin-3-yl}prop-2-enoic acid
C23 H20 Cl2 N2 O3
XJXAZWMUTUJRMD-KFRNIWOLSA-N
FTT
Query on FTT

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A],
N [auth B],
O [auth B]
3-HYDROXY-TETRADECANOIC ACID
C14 H28 O3
ATRNZOYKSNPPBF-CYBMUJFWSA-N
MYR
Query on MYR

Download Ideal Coordinates CCD File 
P [auth B]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
DAO
Query on DAO

Download Ideal Coordinates CCD File 
F [auth A]LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
M [auth B],
Q [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 256.286α = 90
b = 89.786β = 91.29
c = 72.509γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.3: 2018-09-12
    Changes: Data collection, Database references, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-03-13
    Changes: Data collection, Database references, Derived calculations, Structure summary