1K9J

Complex of DC-SIGNR and GlcNAc2Man3

• PDB DOI: https://doi.org/10.2210/pdb1K9J/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: 1.90 Å
• R-Value Free: 0.240 
• R-Value Work: 0.194 

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: https://doi.org/10.1126/science.1066371
• Primary Citation of Related Structures:  
  1K9I, 1K9J


• 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.

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: 33.45 kDa 
• Atom Count: 2,430 
• Modelled Residue Count: 258 
• Deposited Residue Count: 278 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mDC-SIGN2 TYPE I ISOFORM	A, B	139	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2X3 (Homo sapiens) Explore Q9H2X3  Go to UniProtKB:  Q9H2X3
PHAROS:  Q9H2X3 GTEx:  ENSG00000104938

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	C	5		N/A
Glycosylation Resources
GlyTouCan:  G19266OP GlyCosmos:  G19266OP GlyGen:  G19266OP

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
MAN	BindingDB:  1K9J	IC50: 3.39e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.240 
• R-Value Work: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.226	α = 90
b = 57.039	β = 90
c = 89.263	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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: 2008-04-27
  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
• Version 2.1: 2024-11-06
  Changes: Data collection, Database references, Structure summary