4S0F | pdb_00004s0f

Crystal structure of the peptidase-containing ABC transporter PCAT1 E648Q mutant complexed with ATPgS in an occluded conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.51 Å
  • R-Value Free: 
    0.314 (Depositor), 0.333 (DCC) 
  • R-Value Work: 
    0.300 (Depositor), 0.332 (DCC) 
  • R-Value Observed: 
    0.301 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of a polypeptide processing and secretion transporter.

Lin, D.Y.Huang, S.Chen, J.

(2015) Nature 523: 425-430

  • DOI: https://doi.org/10.1038/nature14623
  • Primary Citation Related Structures: 
    4RY2, 4S0F

  • PubMed Abstract: 

    Bacteria secrete peptides and proteins to communicate, to poison competitors, and to manipulate host cells. Among the various protein-translocation machineries, the peptidase-containing ATP-binding cassette transporters (PCATs) are appealingly simple. Each PCAT contains two peptidase domains that cleave the secretion signal from the substrate, two transmembrane domains that form a translocation pathway, and two nucleotide-binding domains that hydrolyse ATP. In Gram-positive bacteria, PCATs function both as maturation proteases and exporters for quorum-sensing or antimicrobial polypeptides. In Gram-negative bacteria, PCATs interact with two other membrane proteins to form the type 1 secretion system. Here we present crystal structures of PCAT1 from Clostridium thermocellum in two different conformations. These structures, accompanied by biochemical data, show that the translocation pathway is a large α-helical barrel sufficient to accommodate small folded proteins. ATP binding alternates access to the transmembrane pathway and also regulates the protease activity, thereby coupling substrate processing to translocation.


  • Organizational Affiliation
    • 1] Laboratory of Membrane Biology and Biophysics, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA [2] Howard Hughes Medical Institute, 1230 York Avenue, New York, New York 10065, USA.

Macromolecule Content 

  • Total Structure Weight: 163.41 kDa 
  • Atom Count: 5,636 
  • Modeled Residue Count: 1,130 
  • Deposited Residue Count: 1,460 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ABC-type bacteriocin transporter
A, B
730Acetivibrio thermocellus ATCC 27405Mutation(s): 1 
Gene Names: ABN51770.1Cthe_0534
EC: 3.4.22
Membrane Entity: Yes 
UniProt
Find proteins for A3DCU1 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Explore A3DCU1 
Go to UniProtKB:  A3DCU1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3DCU1
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.51 Å
  • R-Value Free:  0.314 (Depositor), 0.333 (DCC) 
  • R-Value Work:  0.300 (Depositor), 0.332 (DCC) 
  • R-Value Observed: 0.301 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 230α = 90
b = 230β = 90
c = 89.4γ = 90
Software Package:
Software NamePurpose
JBluIce-EPICSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-08-05
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description