Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D5  (3D View)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 2 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 82.78 kDa 
• Atom Count: 5910 
• Modelled Residue Count: 670 
• Deposited Residue Count: 675 
• Unique protein chains: 1

1MUQ

X-ray Crystal Structure of Rattlesnake Venom Complexed With Thiodigalactoside

• PDB DOI: 10.2210/pdb1MUQ/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Crotalus atrox
• Mutation(s): No 


• Deposited: 2002-09-24 Released: 2003-07-01 
• Deposition Author(s): Walker, J.R., Nagar, B., Young, N.M., Hirama, T., Rini, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.257 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

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

• PubMed: 15049685 
• DOI: 10.1021/bi035871a
• Primary Citation of 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.

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Related Citations: 

• Isolation and characterization of three Ca2+-dependent beta-galactoside-specific lectins from snake venoms
  Gartner, T.K., Ogilvie, M.L.
  (1984) Biochem J 224: 301

• Complete primary structure of a galactose-specific lectin from the venom of the rattlesnake Crotalus atrox. Homologies with Ca2(+)-dependent-type lectins
  Hirabayashi, J.T., Kusunoki, T., Kasai, K.
  (1991) J Biol Chem 266: 2320

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactose-specific lectin	A, B, C, D, E	135	Crotalus atrox	Mutation(s): 0
UniProt
Find proteins for P21963 (Crotalus atrox) Explore P21963  Go to UniProtKB:  P21963

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
1-thio-beta-D-galactopyranose-(1-1)-beta-D-galactopyranose	F [auth G]	2	N/A	N/A
Glycosylation Resources
GlyTouCan:  G61532BD GlyCosmos:  G61532BD

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GAL	I [auth A], N [auth C], S [auth E]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
CA	G [auth A], J [auth B], L [auth C], O [auth D], Q [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	H [auth A], K [auth B], M [auth C], P [auth D], R [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900027	F [auth G]	thiodigalactoside	Oligosaccharide / Substrate analog		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.257 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.454	α = 90
b = 151.234	β = 90
c = 95.014	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASES	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-09-24 
• Released Date: 2003-07-01 
Deposition Author(s): Walker, J.R., Nagar, B., Young, N.M., Hirama, T., Rini, J.M.

Revision History  

• Version 1.0: 2003-07-01
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 3.0: 2020-10-14
  Changes: Atomic model, Data collection, Derived calculations, Structure summary