Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Macromolecule Content

• Total Structure Weight: 132.57 kDa 
• Atom Count: 8,732 
• Modelled Residue Count: 1,008 
• Deposited Residue Count: 1,104 
• Unique protein chains: 1

 1SL6

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

• PDB DOI:  https://doi.org/10.2210/pdb1SL6/pdb

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


• Deposited: 2004-03-05 Released: 2004-06-15 
• Deposition Author(s): Guo, Y., Feinberg, H., Conroy, E., Mitchell, D.A., Alvarez, R., Blixt, O., Taylor, M.E., Weis, W.I., Drickamer, K.

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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 

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

• PubMed: 15195147 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-type lectin DC-SIGNR	A, B, C, D, E, F	184	Homo sapiens	Mutation(s): 0  Gene Names: CLEC4M, CD209L, CD209L1, CD299
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2X3 (Homo sapiens) Explore Q9H2X3  Go to UniProtKB:  Q9H2X3
PHAROS:  Q9H2X3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose	G, H, I, J, K, L	3		N/A
Glycosylation Resources
GlyTouCan:  G51591NI GlyCosmos:  G51591NI GlyGen:  G51591NI

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900120	G, H, I, J, K, L	Lewis X antigen, alpha anomer	Oligosaccharide / 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 = 153.75	α = 90
b = 153.75	β = 90
c = 128.702	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-15 
Deposition Author(s): Guo, Y., Feinberg, H., Conroy, E., Mitchell, D.A., Alvarez, R., Blixt, O., Taylor, M.E., Weis, W.I., Drickamer, K.

Revision History  

• 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