5TV4

3D cryo-EM reconstruction of nucleotide-free MsbA in lipid nanodisc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural basis of MsbA-mediated lipopolysaccharide transport.

Mi, W.Li, Y.Yoon, S.H.Ernst, R.K.Walz, T.Liao, M.

(2017) Nature 549: 233-237

  • DOI: https://doi.org/10.1038/nature23649
  • Primary Citation of Related Structures:  
    5TTP, 5TV4

  • PubMed Abstract: 

    Lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria is critical for the assembly of their cell envelopes. LPS synthesized in the cytoplasmic leaflet of the inner membrane is flipped to the periplasmic leaflet by MsbA, an ATP-binding cassette transporter. Despite substantial efforts, the structural mechanisms underlying MsbA-driven LPS flipping remain elusive. Here we use single-particle cryo-electron microscopy to elucidate the structures of lipid-nanodisc-embedded MsbA in three functional states. The 4.2 Å-resolution structure of the transmembrane domains of nucleotide-free MsbA reveals that LPS binds deep inside MsbA at the height of the periplasmic leaflet, establishing extensive hydrophilic and hydrophobic interactions with MsbA. Two sub-nanometre-resolution structures of MsbA with ADP-vanadate and ADP reveal an unprecedented closed and an inward-facing conformation, respectively. Our study uncovers the structural basis for LPS recognition, delineates the conformational transitions of MsbA to flip LPS, and paves the way for structural characterization of other lipid flippases.


  • Organizational Affiliation

    Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, 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
605Escherichia coli O157:H7Mutation(s): 0 
Gene Names: msbAZ1260ECs0997
EC: 3.6.3
Membrane Entity: Yes 
UniProt
Find proteins for P60752 (Escherichia coli (strain K12))
Explore P60752 
Go to UniProtKB:  P60752
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60752
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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-alpha-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose
C
7N/A
Glycosylation Resources
GlyTouCan:  G75876QI
GlyCosmos:  G75876QI
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FTT
Query on FTT

Download Ideal Coordinates CCD File 
H [auth B],
J [auth B],
L [auth B],
M [auth B]
3-HYDROXY-TETRADECANOIC ACID
C14 H28 O3
ATRNZOYKSNPPBF-CYBMUJFWSA-N
MYR
Query on MYR

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

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

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Derived calculations
  • Version 1.3: 2019-11-06
    Changes: Data collection, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary