3B5Y

Crystal Structure of MsbA from Salmonella typhimurium with AMPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å
  • R-Value Free: 0.343 
  • R-Value Work: 0.295 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Flexibility in the ABC transporter MsbA: Alternating access with a twist.

Ward, A.Reyes, C.L.Yu, J.Roth, C.B.Chang, G.

(2007) Proc.Natl.Acad.Sci.Usa 104: 19005-19010

  • DOI: 10.1073/pnas.0709388104
  • Primary Citation of Related Structures:  3B5W, 3B5X, 3B5Z, 3B60

  • PubMed Abstract: 
  • ATP-binding cassette (ABC) transporters are integral membrane proteins that translocate a wide variety of substrates across cellular membranes and are conserved from bacteria to humans. Here we compare four x-ray structures of the bacterial ABC lipid ...

    ATP-binding cassette (ABC) transporters are integral membrane proteins that translocate a wide variety of substrates across cellular membranes and are conserved from bacteria to humans. Here we compare four x-ray structures of the bacterial ABC lipid flippase, MsbA, trapped in different conformations, two nucleotide-bound structures and two in the absence of nucleotide. Comparison of the nucleotide-free conformations of MsbA reveals a flexible hinge formed by extracellular loops 2 and 3. This hinge allows the nucleotide-binding domains to disassociate while the ATP-binding half sites remain facing each other. The binding of the nucleotide causes a packing rearrangement of the transmembrane helices and changes the accessibility of the transporter from cytoplasmic (inward) facing to extracellular (outward) facing. The inward and outward openings are mediated by two different sets of transmembrane helix interactions. Altogether, the conformational changes between these structures suggest that large ranges of motion may be required for substrate transport.


    Organizational Affiliation

    Departments of Cell Biology and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, CB-105, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipid A export ATP-binding/permease protein msbA
A, B, C, D
582Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Gene Names: msbA
EC: 3.6.3.-
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
MsbA Lipid "flippase" with bound AMPPNP
Find proteins for P63359 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P63359
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ANPKi: 10000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å
  • R-Value Free: 0.343 
  • R-Value Work: 0.295 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 262.929α = 90.00
b = 121.236β = 121.89
c = 173.119γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
PHASESphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance