4OW2 | pdb_00004ow2

YopM from Yersinia enterocolitica WA-314


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.201 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Immunosuppressive Yersinia Effector YopM Binds DEAD Box Helicase DDX3 to Control Ribosomal S6 Kinase in the Nucleus of Host Cells.

Berneking, L.Schnapp, M.Rumm, A.Trasak, C.Ruckdeschel, K.Alawi, M.Grundhoff, A.Kikhney, A.G.Koch-Nolte, F.Buck, F.Perbandt, M.Betzel, C.Svergun, D.I.Hentschke, M.Aepfelbacher, M.

(2016) PLoS Pathog 12: e1005660-e1005660

  • DOI: https://doi.org/10.1371/journal.ppat.1005660
  • Primary Citation Related Structures: 
    4OW2

  • PubMed Abstract: 

    Yersinia outer protein M (YopM) is a crucial immunosuppressive effector of the plaque agent Yersinia pestis and other pathogenic Yersinia species. YopM enters the nucleus of host cells but neither the mechanisms governing its nucleocytoplasmic shuttling nor its intranuclear activities are known. Here we identify the DEAD-box helicase 3 (DDX3) as a novel interaction partner of Y. enterocolitica YopM and present the three-dimensional structure of a YopM:DDX3 complex. Knockdown of DDX3 or inhibition of the exportin chromosomal maintenance 1 (CRM1) increased the nuclear level of YopM suggesting that YopM exploits DDX3 to exit the nucleus via the CRM1 export pathway. Increased nuclear YopM levels caused enhanced phosphorylation of Ribosomal S6 Kinase 1 (RSK1) in the nucleus. In Y. enterocolitica infected primary human macrophages YopM increased the level of Interleukin-10 (IL-10) mRNA and this effect required interaction of YopM with RSK and was enhanced by blocking YopM's nuclear export. We propose that the DDX3/CRM1 mediated nucleocytoplasmic shuttling of YopM determines the extent of phosphorylation of RSK in the nucleus to control transcription of immunosuppressive cytokines.


  • Organizational Affiliation
    • Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 201.44 kDa 
  • Atom Count: 14,226 
  • Modeled Residue Count: 1,792 
  • Deposited Residue Count: 1,792 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Yop effector YopM
A, B, C, D
448Yersinia enterocolitica subsp. enterocolitica WA-314Mutation(s): 0 
Gene Names: YWA314_20912
UniProt
Find proteins for A0A0J9X1Z0 (Yersinia enterocolitica subsp. enterocolitica WA-314)
Explore A0A0J9X1Z0 
Go to UniProtKB:  A0A0J9X1Z0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0J9X1Z0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.847α = 90
b = 126.29β = 118.26
c = 139.933γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-08-05
    Changes: Derived calculations
  • Version 1.2: 2018-03-07
    Changes: Data collection, Derived calculations, Source and taxonomy
  • Version 1.3: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-10-23
    Changes: Structure summary