1JZN | pdb_00001jzn

crystal structure of a galactose-specific C-type lectin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.251 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.198 (Depositor) 
  • R-Value Observed: 
    0.198 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1JZN

This is version 2.1 of the entry. See complete history

Literature

X-ray Crystal Structure of a Galactose-Specific C-Type Lectin Possessing a Novel Decameric Quaternary Structure.

Walker, J.R.Nagar, B.Young, N.M.Hirama, T.Rini, J.M.

(2004) Biochemistry 43: 3783-3792

  • DOI: https://doi.org/10.1021/bi035871a
  • Primary Citation Related Structures: 
    1JZN, 1MUQ

  • PubMed Abstract: 

    Rattlesnake venom lectin (RSL) from the western diamondback rattlesnake (Crotalus atrox) is an oligomeric galactose-specific C-type lectin. The X-ray crystal structure of RSL, in complex with lactose and thiodigalactoside, at 2.2 and 2.3 A resolution, respectively, reveals a decameric protein composed of two 5-fold symmetric pentamers arranged in a staggered, back-to-back orientation. Each monomer corresponds to a single canonical C-type lectin carbohydrate recognition domain devoid of accessory domains and is disulfide-bonded to a monomer in the other pentamer. The structure is the first example of that of a carbohydrate complex of a vertebrate galactose-specific C-type lectin. The 10 carbohydrate-binding sites, located on the rim of the decamer, suggest a role for multivalent interactions and a mechanism for RSL's ability to promote receptor cross-linking and cell aggregation.


  • Organizational Affiliation
    • Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.

Macromolecule Content 

  • Total Structure Weight: 83.62 kDa 
  • Atom Count: 6,395 
  • Modeled Residue Count: 675 
  • Deposited Residue Count: 675 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Galactose-specific lectin
A, B, C, D, E
135Crotalus atroxMutation(s): 0 
UniProt
Find proteins for P21963 (Crotalus atrox)
Explore P21963 
Go to UniProtKB:  P21963
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21963
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
F, G, H, I, J
2N/A
Glycosylation Resources
GlyTouCan: G84224TW
GlyCosmos: G84224TW
GlyGen: G84224TW

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
K [auth A],
M [auth B],
P [auth C],
R [auth D],
T [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



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

Query on NA



Download:Ideal Coordinates CCD File
L [auth A],
N [auth B],
Q [auth C],
S [auth D],
U [auth E]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.251 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.198 (Depositor) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.309α = 90
b = 178.486β = 90
c = 137.832γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary