3B5Z

Crystal Structure of MsbA from Salmonella typhimurium with ADP Vanadate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.362 
  • R-Value Work: 0.336 

wwPDB Validation 3D Report Full Report


This is version 1.3 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 U S A 104: 19005-19010

  • DOI: 10.1073/pnas.0709388104
  • Primary Citation of Related Structures:  
    3B5W, 3B5X, 3B5Y, 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lipid A export ATP-binding/permease protein msbAA, B, C, D582Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: msbA
EC: 3.6.3 (PDB Primary Data), 7.5.2.6 (UniProt)
Membrane protein
Mpstruc
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))
Explore P63359 
Go to UniProtKB:  P63359
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A, B, C, D
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
VO4
Query on VO4

Download CCD File 
A, B, C, D
VANADATE ION
O4 V
LSGOVYNHVSXFFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.362 
  • R-Value Work: 0.336 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 267.169α = 90
b = 121.103β = 121.57
c = 176.744γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-05-29
    Changes: Non-polymer description
  • Version 1.3: 2013-06-05
    Changes: Derived calculations, Non-polymer description