Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.21 kDa 
• Atom Count: 1252 
• Residue Count: 132 
• Unique protein chains: 1

2IT6

Crystal Structure of DCSIGN-CRD with man2

• DOI: 10.2210/pdb2IT6/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-10-19 Released: 2006-12-05 
• Deposition Author(s): Weis, W.I., Feinberg, H., Castelli, R., Drickamer, K., Seeberger, P.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.241 
• R-Value Work: 0.196 

Literature

Multiple modes of binding enhance the affinity of DC-SIGN for high mannose N-linked glycans found on viral glycoproteins.

Feinberg, H., Castelli, R., Drickamer, K., Seeberger, P.H., Weis, W.I.

(2007) J Biol Chem 282: 4202-4209

• PubMed: 17150970 
• DOI: 10.1074/jbc.M609689200
• Primary Citation of Related Structures:  
  2IT6, 2IT5


• PubMed Abstract: 
  

The dendritic cell surface receptor DC-SIGN and the closely related endothelial cell receptor DC-SIGNR specifically recognize high mannose N-linked carbohydrates on viral pathogens. Previous studies have shown that these receptors bind the outer trimannose branch Manalpha1-3[Manalpha1-6]Manalpha present in high mannose structures. Although the trimannoside binds to DC-SIGN or DC-SIGNR more strongly than mannose, additional affinity enhancements are observed in the presence of one or more Manalpha1-2Manalpha moieties on the nonreducing termini of oligomannose structures. The molecular basis of this enhancement has been investigated by determining crystal structures of DC-SIGN bound to a synthetic six-mannose fragment of a high mannose N-linked oligosaccharide, Manalpha1-2Manalpha1-3[Manalpha1-2Manalpha1-6]Manalpha1-6Man and to the disaccharide Manalpha1-2Man. The structures reveal mixtures of two binding modes in each case. Each mode features typical C-type lectin binding at the principal Ca2+-binding site by one mannose residue. In addition, other sugar residues form contacts unique to each binding mode. These results suggest that the affinity enhancement displayed toward oligosaccharides decorated with the Manalpha1-2Manalpha structure is due in part to multiple binding modes at the primary Ca2+ site, which provide both additional contacts and a statistical (entropic) enhancement of binding.

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Organizational Affiliation: 

Departments of Structural Biology and Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CD209 antigen	A	155	Homo sapiens	Mutation(s): 0  Gene Names: CD209, CLEC4L
Find proteins for Q9NNX6 (Homo sapiens) Explore Q9NNX6  Go to UniProtKB:  Q9NNX6
NIH Common Fund Data Resources
PHAROS:  Q9NNX6 GTEx:  ENSG00000090659

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	B	2		N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900111	B	2alpha-alpha-mannobiose	Oligosaccharide /  Metabolism		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.241 
• R-Value Work: 0.196 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.64	α = 90
b = 55.64	β = 90
c = 53.2	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-10-19 
• Released Date: 2006-12-05 
Deposition Author(s): Weis, W.I., Feinberg, H., Castelli, R., Drickamer, K., Seeberger, P.H.

Revision History 

• Version 1.0: 2006-12-05
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary