Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 183.93 kDa 
• Atom Count: 11035 
• Modelled Residue Count: 1283 
• Deposited Residue Count: 1560 
• Unique protein chains: 1

1K9I

Complex of DC-SIGN and GlcNAc2Man3

• DOI: 10.2210/pdb1K9I/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-10-29 Released: 2001-12-21 
• Deposition Author(s): Feinberg, H., Mitchell, D.A., Drickamer, K., Weis, W.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.258 
• R-Value Work: 0.213 

Literature

Structural basis for selective recognition of oligosaccharides by DC-SIGN and DC-SIGNR.

Feinberg, H., Mitchell, D.A., Drickamer, K., Weis, W.I.

(2001) Science 294: 2163-2166

• PubMed: 11739956 
• DOI: 10.1126/science.1066371
• Primary Citation of Related Structures:  
  1K9J, 1K9I


• PubMed Abstract: 
  

Dendritic cell specific intracellular adhesion molecule-3 (ICAM-3) grabbing nonintegrin (DC-SIGN), a C-type lectin present on the surface of dendritic cells, mediates the initial interaction of dendritic cells with T cells by binding to ICAM-3. DC-SIGN and DC-SIGNR, a related receptor found on the endothelium of liver sinusoids, placental capillaries, and lymph nodes, bind to oligosaccharides that are present on the envelope of human immunodeficiency virus (HIV), an interaction that strongly promotes viral infection of T cells. Crystal structures of carbohydrate-recognition domains of DC-SIGN and of DC-SIGNR bound to oligosaccharide, in combination with binding studies, reveal that these receptors selectively recognize endogenous high-mannose oligosaccharides and may represent a new avenue for developing HIV prophylactics.

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Organizational Affiliation: 

Department of Structural Biology, University School of Medicine, Stanford, CA 94305, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mDC-SIGN1B type I isoform	A,  B,  C,  D,  E,  F,  G,  H,  I,  J	156	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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose	K, L, M, N, O	5		N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.258 
• R-Value Work: 0.213 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.805	α = 90
b = 148.161	β = 91.03
c = 112.991	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
COMO	phasing
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-10-29 
• Released Date: 2001-12-21 
Deposition Author(s): Feinberg, H., Mitchell, D.A., Drickamer, K., Weis, W.I.

Revision History  

• Version 1.0: 2001-12-21
  Type: Initial release
  
• Version 1.1: 2007-10-16
  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: Atomic model, Data collection, Derived calculations, Structure summary