1XKP

Crystal structure of the virulence factor YopN in complex with its heterodimeric chaperone SycN-YscB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Three-dimensional structure of a macromolecular assembly that regulates type III secretion in Yersinia pestis.

Schubot, F.D.Jackson, M.W.Penrose, K.J.Cherry, S.Tropea, J.E.Plano, G.V.Waugh, D.S.

(2005) J Mol Biol 346: 1147-1161

  • DOI: 10.1016/j.jmb.2004.12.036
  • Primary Citation of Related Structures:  
    1XKP, 1XL3

  • PubMed Abstract: 
  • Yersinia pestis, the causative agent of plague, utilizes a type III secretion system (T3SS) to inject effector proteins directly into the cytosol of mammalian cells where they interfere with signal transduction pathways that regulate actin cytoskeleton dynamics and inflammation, thereby enabling the bacterium to avoid engulfment and destruction by macrophages ...

    Yersinia pestis, the causative agent of plague, utilizes a type III secretion system (T3SS) to inject effector proteins directly into the cytosol of mammalian cells where they interfere with signal transduction pathways that regulate actin cytoskeleton dynamics and inflammation, thereby enabling the bacterium to avoid engulfment and destruction by macrophages. Type III secretion normally does not occur in the absence of close contact with eukaryotic cells. Negative regulation is mediated in part by a multiprotein complex that has been proposed to act as a physical impediment to type III secretion by blocking the entrance to the secretion apparatus prior to contact with mammalian cells. This complex is composed of YopN, its heterodimeric secretion chaperone SycN-YscB, and TyeA. Here, we report two crystal structures of YopN in complex with its heterodimeric secretion chaperone SycN-YscB and the co-regulatory protein TyeA, respectively. By merging these two overlapping structures, it was possible to construct a credible theoretical model of the YopN-SycN-YscB-TyeA complex. The modeled assembly features the secretion signaling elements of YopN at one end of an elongated structure and the secretion regulating TyeA binding site at the other. A patch of highly conserved residues on the surface of the C-terminal alpha-helix of TyeA may mediate its interaction with structural components of the secretion apparatus. Conserved arginine residues that reside inside a prominent cavity at the dimer interface of SycN-YscB were mutated in order to investigate whether they play a role in targeting the YopN-chaperone complex to the type III secretion apparatus. One of the mutants exhibited a phenotype that is consistent with this hypothesis.


    Related Citations: 
    • A pivotal role for reductive methylation in the de novo crystallization of a ternary complex composed of Yersinia pestis virulence factors YopN, SycN and YscB
      Schubot, F.D., Waugh, D.S.
      (2004) Acta Crystallogr D Biol Crystallogr 60: 1981

    Organizational Affiliation

    Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702-1201, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
putative membrane-bound Yop targeting protein YopNA246Yersinia pestisMutation(s): 16 
Gene Names: yopNlcrEYPCD1.39cy5039y0042YP_pCD44
UniProt
Find proteins for P68640 (Yersinia pestis)
Explore P68640 
Go to UniProtKB:  P68640
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68640
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Chaperone protein sycNB124Yersinia pestisMutation(s): 3 
Gene Names: sycNYPCD1.37cy5041y0044YP_pCD46
UniProt
Find proteins for P61380 (Yersinia pestis)
Explore P61380 
Go to UniProtKB:  P61380
Entity Groups  
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UniProt GroupP61380
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Chaperone protein yscBC143Yersinia pestisMutation(s): 5 
Gene Names: yscBYPCD1.51y5027y0030YP_pCD32
UniProt
Find proteins for Q56973 (Yersinia pestis)
Explore Q56973 
Go to UniProtKB:  Q56973
Entity Groups  
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UniProt GroupQ56973
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
A L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.718α = 90
b = 60.718β = 90
c = 140.419γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations