6CSX

Single particles Cryo-EM structure of AcrB D407A associated with lipid bilayer at 3.0 Angstrom

• PDB DOI:  https://doi.org/10.2210/pdb6CSX/pdb
• EM Map EMD-7609: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2018-03-21 Released: 2018-12-05 
• Deposition Author(s): Qiu, W., Fu, Z., Guo, Y.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 30509977 
• DOI: https://doi.org/10.1073/pnas.1812526115
• Primary Citation of Related Structures:  
  6BAJ, 6CSX


• 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 3.2-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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 357.46 kDa 
• Atom Count: 23,232 
• Modelled Residue Count: 2,999 
• Deposited Residue Count: 3,171 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux pump subunit AcrB	A [auth B], B [auth C], C [auth A]	1,057	Escherichia coli K-12	Mutation(s): 1  Gene Names: acrB, acrE, b0462, JW0451 Membrane Entity: Yes
UniProt
Find proteins for P31224 (Escherichia coli (strain K12)) Explore P31224  Go to UniProtKB:  P31224

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PTY	D [auth B], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], L [auth C], M [auth C], N [auth C], O [auth C], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	PHOSPHATIDYLETHANOLAMINE C40 H80 N O8 P NJGIRBISCGPRPF-KXQOOQHDSA-N
D12	K [auth B]	DODECANE C12 H26 SNRUBQQJIBEYMU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-05 
Deposition Author(s): Qiu, W., Fu, Z., Guo, Y.

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Funding Organization	Location	Grant Number
Other government	United States	Startup

Revision History  

• Version 1.0: 2018-12-05
  Type: Initial release
  
• Version 1.1: 2018-12-19
  Changes: Data collection, Database references
• Version 1.2: 2019-01-02
  Changes: Data collection, Database references