1X99 | pdb_00001x99

X-ray crystal structure of Xerocomus chrysenteron lectin XCL at 1.4 Angstroms resolution, mutated at Q46M, V54M, L58M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.187 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.174 (Depositor) 
  • R-Value Observed: 
    0.174 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1X99

This is version 1.4 of the entry. See complete history

Literature

A New Lectin Family with Structure Similarity to Actinoporins Revealed by the Crystal Structure of Xerocomus chrysenteron Lectin XCL

Birck, C.Damian, L.Marty-Detraves, C.Lougarre, A.Schulze-Briese, C.Koehl, P.Fournier, D.Paquereau, L.Samama, J.P.

(2004) J Mol Biology 344: 1409-1420

  • DOI: https://doi.org/10.1016/j.jmb.2004.10.007
  • Primary Citation Related Structures: 
    1X99, 1XI0

  • PubMed Abstract: 

    A newly defined family of fungal lectins displays no significant sequence similarity to any protein in the databases. These proteins, made of about 140 amino acid residues, have sequence identities ranging from 38% to 65% and share binding specificity to N-acetyl galactosamine. One member of this family, the lectin XCL from Xerocomus chrysenteron, induces drastic changes in the actin cytoskeleton after sugar binding at the cell surface and internalization, and has potent insecticidal activity. The crystal structure of XCL to 1.4 A resolution reveals the architecture of this new lectin family. The fold of the protein is not related to any of the several lectin folds documented so far. Unexpectedly, the structure similarity is significant with actinoporins, a family of pore-forming toxins. The specific structural features and sequence signatures in each protein family suggest a potential sugar binding site in XCL and a possible evolutionary relationship between these proteins. Finally, the tetrameric assembly of XCL reveals a complex network of protomer-protomer interfaces and generates a large, hydrated cavity of 1000 A3, which may become accessible to larger solutes after a small conformational change of the protein.


  • Organizational Affiliation
    • Département de Génomique et Biologie Structurales, IGBMC CNRS/INSERM/ULP, 1 rue Laurent Fries, BP 10142, 67404-Illkirch CU Strasbourg, France.

Macromolecule Content 

  • Total Structure Weight: 33.21 kDa 
  • Atom Count: 2,434 
  • Modeled Residue Count: 288 
  • Deposited Residue Count: 290 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
lectin
A, B
145Xerocomellus chrysenteronMutation(s): 4 
UniProt
Find proteins for Q8WZC9 (Xerocomellus chrysenteron)
Explore Q8WZC9 
Go to UniProtKB:  Q8WZC9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WZC9
Sequence Annotations
Expand
Reference Sequence

Small Molecules

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

Query on SO4



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

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.187 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.174 (Depositor) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.153α = 90
b = 59.153β = 90
c = 149.663γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-10-16
    Changes: Data collection, Structure summary