1SL6

Crystal Structure of a fragment of DC-SIGNR (containg the carbohydrate recognition domain and two repeats of the neck) complexed with Lewis-x.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural basis for distinct ligand-binding and targeting properties of the receptors DC-SIGN and DC-SIGNR

Guo, Y.Feinberg, H.Conroy, E.Mitchell, D.A.Alvarez, R.Blixt, O.Taylor, M.E.Weis, W.I.Drickamer, K.

(2004) Nat Struct Mol Biol 11: 591-598

  • DOI: 10.1038/nsmb784
  • Primary Citation of Related Structures:  
    1SL4, 1SL5, 1SL6

  • PubMed Abstract: 
  • Both the dendritic cell receptor DC-SIGN and the closely related endothelial cell receptor DC-SIGNR bind human immunodeficiency virus and enhance infection. However, biochemical and structural comparison of these receptors now reveals that they have very different physiological functions ...

    Both the dendritic cell receptor DC-SIGN and the closely related endothelial cell receptor DC-SIGNR bind human immunodeficiency virus and enhance infection. However, biochemical and structural comparison of these receptors now reveals that they have very different physiological functions. By screening an extensive glycan array, we demonstrated that DC-SIGN and DC-SIGNR have distinct ligand-binding properties. Our structural and mutagenesis data explain how both receptors bind high-mannose oligosaccharides on enveloped viruses and why only DC-SIGN binds blood group antigens, including those present on microorganisms. DC-SIGN mediates endocytosis, trafficking as a recycling receptor and releasing ligand at endosomal pH, whereas DC-SIGNR does not release ligand at low pH or mediate endocytosis. Thus, whereas DC-SIGN has dual ligand-binding properties and functions both in adhesion and in endocytosis of pathogens, DC-SIGNR binds a restricted set of ligands and has only the properties of an adhesion receptor.


    Organizational Affiliation

    Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-type lectin DC-SIGNR
A, B, C, D, E, F
A, B, C, D, E, F
184Homo sapiensMutation(s): 0 
Gene Names: CLEC4MCD209LCD209L1CD299
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2X3 (Homo sapiens)
Explore Q9H2X3 
Go to UniProtKB:  Q9H2X3
PHAROS:  Q9H2X3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H2X3
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose
G, H, I, J, K, L
G, H, I, J, K, L
3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G51591NI
GlyCosmos:  G51591NI
GlyGen:  G51591NI
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 D],
CA [auth E],
DA [auth E],
EA [auth E],
AA [auth D],
BA [auth D],
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth E],
GA [auth F],
HA [auth F],
IA [auth F],
JA [auth F],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth D],
Z [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900120
Query on PRD_900120
G, H, I, J, K, LLewis X antigen, alpha anomerOligosaccharide / Antigen Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.75α = 90
b = 153.75β = 90
c = 128.702γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
COMOphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    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