6YHK | pdb_00006yhk

Crystal structure of full-length CNFy (C866S) from Yersinia pseudotuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.242 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 6YHK

This is version 1.3 of the entry. See complete history

Literature

Crystal structure of bacterial cytotoxic necrotizing factor CNF Y reveals molecular building blocks for intoxication.

Chaoprasid, P.Lukat, P.Muhlen, S.Heidler, T.Gazdag, E.M.Dong, S.Bi, W.Ruter, C.Kirchenwitz, M.Steffen, A.Jansch, L.Stradal, T.E.B.Dersch, P.Blankenfeldt, W.

(2021) EMBO J 40: e105202-e105202

  • DOI: https://doi.org/10.15252/embj.2020105202
  • Primary Citation Related Structures: 
    6YHK, 6YHL, 6YHM, 6YHN

  • PubMed Abstract: 

    Cytotoxic necrotizing factors (CNFs) are bacterial single-chain exotoxins that modulate cytokinetic/oncogenic and inflammatory processes through activation of host cell Rho GTPases. To achieve this, they are secreted, bind surface receptors to induce endocytosis and translocate a catalytic unit into the cytosol to intoxicate host cells. A three-dimensional structure that provides insight into the underlying mechanisms is still lacking. Here, we determined the crystal structure of full-length Yersinia pseudotuberculosis CNF Y . CNF Y consists of five domains (D1-D5), and by integrating structural and functional data, we demonstrate that D1-3 act as export and translocation module for the catalytic unit (D4-5) and for a fused β-lactamase reporter protein. We further found that D4, which possesses structural similarity to ADP-ribosyl transferases, but had no equivalent catalytic activity, changed its position to interact extensively with D5 in the crystal structure of the free D4-5 fragment. This liberates D5 from a semi-blocked conformation in full-length CNF Y , leading to higher deamidation activity. Finally, we identify CNF translocation modules in several uncharacterized fusion proteins, which suggests their usability as a broad-specificity protein delivery tool.


  • Organizational Affiliation
    • Institute of Infectiology, Center for Molecular Biology of Inflammation (ZMBE), University of Münster, Münster, Germany.

Macromolecule Content 

  • Total Structure Weight: 115.82 kDa 
  • Atom Count: 7,921 
  • Modeled Residue Count: 994 
  • Deposited Residue Count: 1,018 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytotoxic necrotizing factor1,018Yersinia pseudotuberculosisMutation(s): 1 
Gene Names: cnf
UniProt
Find proteins for A0A0N9JNY6 (Yersinia pseudotuberculosis)
Explore A0A0N9JNY6 
Go to UniProtKB:  A0A0N9JNY6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0N9JNY6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.242 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.153α = 90
b = 180.416β = 90
c = 220.761γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references
  • Version 1.2: 2021-02-24
    Changes: Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Refinement description