2MSB

STRUCTURE OF A C-TYPE MANNOSE-BINDING PROTEIN COMPLEXED WITH AN OLIGOSACCHARIDE

• PDB DOI: https://doi.org/10.2210/pdb2MSB/pdb

• Classification: LECTIN
• Organism(s): Rattus rattus
• Mutation(s): No 


• Deposited: 1992-07-28 Released: 1993-10-31 
• Deposition Author(s): Weis, W.I., Drickamer, K., Hendrickson, W.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Work: 0.174 
• R-Value Observed: 0.174 

Literature

Structure of a C-type mannose-binding protein complexed with an oligosaccharide.

Weis, W.I., Drickamer, K., Hendrickson, W.A.

(1992) Nature 360: 127-134

• PubMed: 1436090 
• DOI: https://doi.org/10.1038/360127a0
• Primary Citation of Related Structures:  
  2MSB


• PubMed Abstract: 
  

  C-type (Ca(2+)-dependent) animal lectins such as mannose-binding proteins mediate many cell-surface carbohydrate-recognition events. The crystal structure at 1.7 A resolution of the carbohydrate-recognition domain of rat mannose-binding protein complexed with an oligomannose asparaginyl-oligosaccharide reveals that Ca2+ forms coordination bonds with the carbohydrate ligand. Carbohydrate specificity is determined by a network of coordination and hydrogen bonds that stabilizes the ternary complex of protein, Ca2+ and sugar. Two branches of the oligosaccharide crosslink neighbouring carbohydrate-recognition domains in the crystal, enabling multivalent binding to a single oligosaccharide chain to be visualized directly.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26.81 kDa 
• Atom Count: 2,041 
• Modelled Residue Count: 225 
• Deposited Residue Count: 230 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MANNOSE-BINDING PROTEIN-A	A, B	115	Rattus rattus	Mutation(s): 0
UniProt
Find proteins for P19999 (Rattus norvegicus) Explore P19999  Go to UniProtKB:  P19999

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	7		N/A
Glycosylation Resources
GlyTouCan:  G30704AF GlyCosmos:  G30704AF GlyGen:  G30704AF

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Work: 0.174 
• R-Value Observed: 0.174 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.81	α = 90
b = 85.16	β = 97.41
c = 39.55	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): Weis, W.I., Drickamer, K., Hendrickson, W.A.

Revision History  

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary