7RR6 | pdb_00007rr6

Multidrug efflux pump subunit AcrB


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

pH-tunable membrane-active polymers, NCMNP2a- x , and their potential membrane protein applications.

Trinh, T.K.H.Cabezas, A.J.Joshi, S.Catalano, C.Siddique, A.B.Qiu, W.Deshmukh, S.des Georges, A.Guo, Y.

(2023) Chem Sci 14: 7310-7326

  • DOI: https://doi.org/10.1039/d3sc01890c
  • Primary Citation of Related Structures:  
    7RR6, 7RR7, 7RR8

  • PubMed Abstract: 

    Accurate 3D structures of membrane proteins are essential for comprehending their mechanisms of action and designing specific ligands to modulate their activities. However, these structures are still uncommon due to the involvement of detergents in the sample preparation. Recently, membrane-active polymers have emerged as an alternative to detergents, but their incompatibility with low pH and divalent cations has hindered their efficacy. Herein, we describe the design, synthesis, characterization, and application of a new class of pH-tunable membrane-active polymers, NCMNP2a- x . The results demonstrated that NCMNP2a- x could be used for high-resolution single-particle cryo-EM structural analysis of AcrB in various pH conditions and can effectively solubilize Bc TSPO with the function preserved. Molecular dynamic simulation is consistent with experimental data that shed great insights into the working mechanism of this class of polymers. These results demonstrated that NCMNP2a- x might have broad applications in membrane protein research.


  • Organizational Affiliation
    • Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA yguo4@vcu.edu.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multidrug efflux pump subunit AcrBA [auth B],
B [auth C],
C [auth A]
1,057Escherichia 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31224
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PTY (Subject of Investigation/LOI)
Query on PTY

Download Ideal Coordinates CCD File 
CA [auth A]
D [auth B]
DA [auth A]
E [auth B]
EA [auth A]
CA [auth A],
D [auth B],
DA [auth A],
E [auth B],
EA [auth A],
F [auth B],
FA [auth A],
G [auth B],
GA [auth A],
H [auth B],
HA [auth A],
I [auth B],
IA [auth A],
J [auth B],
JA [auth A],
K [auth B],
KA [auth A],
L [auth B],
LA [auth A],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
D12 (Subject of Investigation/LOI)
Query on D12

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
M [auth B]
N [auth B]
O [auth B]
AA [auth C],
BA [auth C],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Y [auth C],
Z [auth C]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM132329
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R35GM133598

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-17
    Type: Initial release
  • Version 1.1: 2024-06-05
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Structure summary