3T53 | pdb_00003t53

Crystal structures of the extrusion state of the CusBA adaptor-transporter complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.37 Å
  • R-Value Free: 
    0.286 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.248 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.250 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Charged Amino Acids (R83, E567, D617, E625, R669, and K678) of CusA Are Required for Metal Ion Transport in the Cus Efflux System.

Su, C.C.Long, F.Lei, H.T.Bolla, J.R.Do, S.V.Rajashankar, K.R.Yu, E.W.

(2012) J Mol Biology 422: 429-441

  • DOI: https://doi.org/10.1016/j.jmb.2012.05.038
  • Primary Citation Related Structures: 
    3T51, 3T53, 3T56, 4DNT, 4DOP

  • PubMed Abstract: 

    Gram-negative bacteria expel various toxic chemicals via tripartite efflux pumps belonging to the resistance-nodulation-cell division superfamily. These pumps span both the inner and outer membranes of the cell. The three components of these tripartite systems are an inner-membrane, substrate-binding transporter (or pump); a periplasmic membrane fusion protein (or adaptor); and an outer-membrane-anchored channel. These three efflux proteins interact in the periplasmic space to form the three-part complexes. We previously presented the crystal structures of both the inner-membrane transporter CusA and membrane fusion protein CusB of the CusCBA tripartite efflux system from Escherichia coli. We also described the co-crystal structure of the CusBA adaptor-transporter, revealing that the trimeric CusA efflux pump assembles with six CusB protein molecules to form the complex CusB(6)-CusA(3). We here report three different conformers of the crystal structures of CusBA-Cu(I), suggesting a mechanism on how Cu(I) binding initiates a sequence of conformational transitions in the transport cycle. Genetic analysis and transport assays indicate that charged residues, in addition to the methionine pairs and clusters, are essential for extruding metal ions out of the cell.


  • Organizational Affiliation
    • Department of Chemistry, Iowa State University, Ames, IA 50011, USA.

Macromolecule Content 

  • Total Structure Weight: 189 kDa 
  • Atom Count: 12,876 
  • Modeled Residue Count: 1,674 
  • Deposited Residue Count: 1,726 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cation efflux system protein CusBA [auth B],
B [auth C]
336Escherichia coli K-12Mutation(s): 0 
Gene Names: b0574cusBJW0563ylcD
Membrane Entity: Yes 
UniProt
Find proteins for P77239 (Escherichia coli (strain K12))
Explore P77239 
Go to UniProtKB:  P77239
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77239
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cation efflux system protein CusAC [auth A]1,054Escherichia coli K-12Mutation(s): 0 
Gene Names: cusAybdEb0575JW0564
Membrane Entity: Yes 
UniProt
Find proteins for P38054 (Escherichia coli (strain K12))
Explore P38054 
Go to UniProtKB:  P38054
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38054
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CU

Query on CU



Download:Ideal Coordinates CCD File
D [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.37 Å
  • R-Value Free:  0.286 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.248 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.250 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.787α = 90
b = 159.787β = 90
c = 683.042γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2012-07-04
    Changes: Database references
  • Version 1.2: 2012-09-05
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations