5L22

PrtD T1SS ABC transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of a Type-1 Secretion System ABC Transporter.

Morgan, J.L.Acheson, J.F.Zimmer, J.

(2017) Structure 25: 522-529

  • DOI: 10.1016/j.str.2017.01.010

  • PubMed Abstract: 
  • Type-1 secretion systems (T1SSs) represent a widespread mode of protein secretion across the cell envelope in Gram-negative bacteria. The T1SS is composed of an inner-membrane ABC transporter, a periplasmic membrane-fusion protein, and an outer-membr ...

    Type-1 secretion systems (T1SSs) represent a widespread mode of protein secretion across the cell envelope in Gram-negative bacteria. The T1SS is composed of an inner-membrane ABC transporter, a periplasmic membrane-fusion protein, and an outer-membrane porin. These three components assemble into a complex spanning both membranes and providing a conduit for the translocation of unfolded polypeptides. We show that ATP hydrolysis and assembly of the entire T1SS complex is necessary for protein secretion. Furthermore, we present a 3.15-Å crystal structure of AaPrtD, the ABC transporter found in the Aquifex aeolicus T1SS. The structure suggests a substrate entry window just above the transporter's nucleotide binding domains. In addition, highly kinked transmembrane helices, which frame a narrow channel not observed in canonical peptide transporters, are likely involved in substrate translocation. Overall, the AaPrtD structure supports a polypeptide transport mechanism distinct from alternating access.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 480 Ray C. Hunt Drive, Charlottesville, VA 22908, USA.,Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 480 Ray C. Hunt Drive, Charlottesville, VA 22908, USA. Electronic address: jochen_zimmer@virginia.edu.,Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 480 Ray C. Hunt Drive, Charlottesville, VA 22908, USA. Electronic address: jlm2qp@virginia.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ABC transporter (HlyB subfamily)
B, A
572Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: abcT5
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
PrtD Type-1 secretion system ABC transporter
Find proteins for O67184 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O67184
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 118.672α = 90.00
b = 97.938β = 100.47
c = 179.823γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
SHELXCDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-03-22
    Type: Database references