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 5B5Q | pdb_00005b5q

1.7 Angstroms structure of ChlaDub1 from Chlamydia Trachomatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.213 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5B5Q

This is version 1.2 of the entry. See complete history. 

Literature

Chlamydia trachomatis-containing vacuole serves as deubiquitination platform to stabilize Mcl-1 and to interfere with host defense

Fischer, A., Harrison, K.S., Ramirez, Y., Auer, D., Chowdhury, S.R., Prusty, B.K., Sauer, F., Dimond, Z., Kisker, C., Scott Hefty, P., Rudel, T.

(2017) Elife 6

  • DOI: https://doi.org/10.7554/eLife.21465
  • Primary Citation Related Structures: 
    5B5Q

  • PubMed Abstract: 

    Obligate intracellular Chlamydia trachomatis replicate in a membrane-bound vacuole called inclusion, which serves as a signaling interface with the host cell. Here, we show that the chlamydial deubiquitinating enzyme (Cdu) 1 localizes in the inclusion membrane and faces the cytosol with the active deubiquitinating enzyme domain. The structure of this domain revealed high similarity to mammalian deubiquitinases with a unique α-helix close to the substrate-binding pocket. We identified the apoptosis regulator Mcl-1 as a target that interacts with Cdu1 and is stabilized by deubiquitination at the chlamydial inclusion. A chlamydial transposon insertion mutant in the Cdu1-encoding gene exhibited increased Mcl-1 and inclusion ubiquitination and reduced Mcl-1 stabilization. Additionally, inactivation of Cdu1 led to increased sensitivity of C. trachomatis for IFNγ and impaired infection in mice. Thus, the chlamydial inclusion serves as an enriched site for a deubiquitinating activity exerting a function in selective stabilization of host proteins and protection from host defense.


  • Organizational Affiliation: 
    • Department of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 56.34 kDa 
  • Atom Count: 4,477 
  • Modeled Residue Count: 488 
  • Deposited Residue Count: 492 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Membrane thiol protease243Chlamydia trachomatisMutation(s): 0 
Gene Names: cdu1, ERS066953_00737
EC: 3.4.22
UniProt
Find proteins for B0B9A0 (Chlamydia trachomatis serovar L2 (strain ATCC VR-902B / DSM 19102 / 434/Bu))
Explore B0B9A0 
Go to UniProtKB:  B0B9A0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0B9A0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Membrane thiol protease249Chlamydia trachomatisMutation(s): 0 
Gene Names: CT868
EC: 3.4.22
UniProt
Find proteins for B0B9A0 (Chlamydia trachomatis serovar L2 (strain ATCC VR-902B / DSM 19102 / 434/Bu))
Explore B0B9A0 
Go to UniProtKB:  B0B9A0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0B9A0
Sequence Annotations
Expand
Reference Sequence

Small Molecules

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

Query on CL



Download:Ideal Coordinates CCD File
C [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.213 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.1α = 90
b = 77.573β = 96.43
c = 68.948γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
GSLS University of WuerzburgGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references