6BAJ

Cryo-EM structure of lipid bilayer in the native cell membrane nanoparticles of AcrB


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and activity of lipid bilayer within a membrane-protein transporter.

Qiu, W.Fu, Z.Xu, G.G.Grassucci, R.A.Zhang, Y.Frank, J.Hendrickson, W.A.Guo, Y.

(2018) Proc Natl Acad Sci U S A 115: 12985-12990

  • DOI: 10.1073/pnas.1812526115
  • Primary Citation of Related Structures:  
    6CSX, 6BAJ

  • PubMed Abstract: 
  • Membrane proteins function in native cell membranes, but extraction into isolated particles is needed for many biochemical and structural analyses. Commonly used detergent-extraction methods destroy naturally associated lipid bilayers. Here, we devised a detergent-free method for preparing cell-membrane nanoparticles to study the multidrug exporter AcrB, by cryo-EM at 3 ...

    Membrane proteins function in native cell membranes, but extraction into isolated particles is needed for many biochemical and structural analyses. Commonly used detergent-extraction methods destroy naturally associated lipid bilayers. Here, we devised a detergent-free method for preparing cell-membrane nanoparticles to study the multidrug exporter AcrB, by cryo-EM at 3.2-Å resolution. We discovered a remarkably well-organized lipid-bilayer structure associated with transmembrane domains of the AcrB trimer. This bilayer patch comprises 24 lipid molecules; inner leaflet chains are packed in a hexagonal array, whereas the outer leaflet has highly irregular but ordered packing. Protein side chains interact with both leaflets and participate in the hexagonal pattern. We suggest that the lipid bilayer supports and harmonizes peristaltic motions through AcrB trimers. In AcrB D407A, a putative proton-relay mutant, lipid bilayer buttresses protein interactions lost in crystal structures after detergent-solubilization. Our detergent-free system preserves lipid-protein interactions for visualization and should be broadly applicable.


    Organizational Affiliation

    Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Multidrug efflux pump subunit AcrBC [auth A], A [auth B], B [auth C]1057Escherichia 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PTY
Query on PTY

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , CA [auth C] , D [auth B] , E [auth B] , F [auth B] , G [auth B] , H [auth B] , 
AA [auth C],  BA [auth C],  CA [auth C],  D [auth B],  E [auth B],  F [auth B],  G [auth B],  H [auth B],  I [auth B],  IA [auth A],  J [auth B],  JA [auth A],  K [auth B],  KA [auth A],  L [auth B],  LA [auth A],  MA [auth A],  NA [auth A],  OA [auth A],  PA [auth A],  QA [auth A],  RA [auth A],  S [auth C],  SA [auth A],  T [auth C],  U [auth C],  V [auth C],  W [auth C],  X [auth C],  Y [auth C],  Z [auth C]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
 Ligand Interaction
D12
Query on D12

Download Ideal Coordinates CCD File 
DA [auth C] , EA [auth C] , FA [auth C] , GA [auth C] , HA [auth C] , M [auth B] , N [auth B] , O [auth B] , 
DA [auth C],  EA [auth C],  FA [auth C],  GA [auth C],  HA [auth C],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  Q [auth B],  R [auth B]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-10-13 
  • Released Date: 2018-12-19 
  • Deposition Author(s): Qiu, W., Fu, Z., Guo, Y.

Funding OrganizationLocationGrant Number
School of Pharmacy, Virginia Commonwealth UniversityUnited States147019
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM29169

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.3: 2020-07-01
    Changes: Database references