1K9I

Complex of DC-SIGN and GlcNAc2Man3


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
mDC-SIGN1B type I isoform
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J
156Homo sapiensMutation(s): 0 
Gene Names: CD209CLEC4L
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NNX6 (Homo sapiens)
Explore Q9NNX6 
Go to UniProtKB:  Q9NNX6
PHAROS:  Q9NNX6
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-mannopyranoseK, L, M, N, O5N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G19266OP
GlyCosmos:  G19266OP
GlyGen:  G19266OP
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth D] , BA [auth E] , CA [auth E] , DA [auth E] , EA [auth F] , FA [auth F] , GA [auth F] , HA [auth G] , 
AA [auth D],  BA [auth E],  CA [auth E],  DA [auth E],  EA [auth F],  FA [auth F],  GA [auth F],  HA [auth G],  IA [auth G],  JA [auth G],  KA [auth H],  LA [auth H],  MA [auth H],  NA [auth I],  OA [auth I],  P [auth A],  PA [auth I],  Q [auth A],  QA [auth J],  R [auth A],  RA [auth J],  S [auth B],  SA [auth J],  T [auth B],  U [auth B],  V [auth C],  W [auth C],  X [auth C],  Y [auth D],  Z [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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 = 106.805α = 90
b = 148.161β = 91.03
c = 112.991γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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