8A9X | pdb_00008a9x

Crystal structure of PulM C-ter domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 
    0.231 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structure and dynamic association of an assembly platform subcomplex of the bacterial type II secretion system.

Dazzoni, R.Li, Y.Lopez-Castilla, A.Brier, S.Mechaly, A.Cordier, F.Haouz, A.Nilges, M.Francetic, O.Bardiaux, B.Izadi-Pruneyre, N.

(2023) Structure 31: 152

  • DOI: https://doi.org/10.1016/j.str.2022.12.003
  • Primary Citation Related Structures: 
    7ZE0, 8A9W, 8A9X, 8AB1

  • PubMed Abstract: 

    Type II secretion systems (T2SSs) allow diderm bacteria to secrete hydrolytic enzymes, adhesins, or toxins important for growth and virulence. To promote secretion of folded proteins, T2SSs assemble periplasmic filaments called pseudopili or endopili at an inner membrane subcomplex, the assembly platform (AP). Here, we combined biophysical approaches, nuclear magnetic resonance (NMR) and X-ray crystallography, to study the Klebsiella AP components PulL and PulM. We determined the structure and associations of their periplasmic domains and describe the structure of the heterodimer formed by their ferredoxin-like domains. We show how structural complementarity and plasticity favor their association during the secretion process. Cysteine scanning and crosslinking data provided additional constraints to build a structural model of the PulL-PulM assembly in the cellular context. Our structural and functional insights, together with the relative cellular abundance of its components, support the role of AP as a dynamic hub that orchestrates pilus polymerization.


  • Organizational Affiliation
    • Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France.

Macromolecule Content 

  • Total Structure Weight: 59.95 kDa 
  • Atom Count: 4,680 
  • Modeled Residue Count: 549 
  • Deposited Residue Count: 560 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Type II secretion system protein M
A, B, C, D, E
A, B, C, D, E, F, G
80Klebsiella oxytocaMutation(s): 0 
Gene Names: DVB85_16620
UniProt
Find proteins for P15752 (Klebsiella pneumoniae)
Explore P15752 
Go to UniProtKB:  P15752
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15752
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free:  0.231 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.85α = 90
b = 135.529β = 90
c = 109.408γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)France19-CE11-0020-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2023-04-12
    Changes: Structure summary
  • Version 1.3: 2024-06-19
    Changes: Data collection