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URL: https://www.rcsb.org/structure/4N34

⇱ RCSB PDB - 4N34: Structure of langerin CRD I313 with alpha-MeGlcNAc

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Structures from the PDB archive		1,062,058
Computed Structure Models (CSM)

 4N34 | pdb_00004n34

Structure of langerin CRD I313 with alpha-MeGlcNAc

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.229 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.176 (Depositor) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 

Literature

Common polymorphisms in human langerin change specificity for glycan ligands.

Feinberg, H., Rowntree, T.J., Tan, S.L., Drickamer, K., Weis, W.I., Taylor, M.E.

(2013) J Biological Chem 288: 36762-36771

  • DOI: https://doi.org/10.1074/jbc.M113.528000
  • Primary Citation Related Structures: 
    4N32, 4N33, 4N34, 4N35, 4N36, 4N37, 4N38

  • PubMed Abstract: 

    Langerin, a C-type lectin on Langerhans cells, mediates carbohydrate-dependent uptake of pathogens in the first step of antigen presentation to the adaptive immune system. Langerin binds a diverse range of carbohydrates including high mannose structures, fucosylated blood group antigens, and glycans with terminal 6-sulfated galactose. Mutagenesis and quantitative binding assays indicate that salt bridges between the sulfate group and two lysine residues compensate for the nonoptimal binding of galactose at the primary Ca(2+) site. A commonly occurring single nucleotide polymorphism (SNP) in human langerin results in change of one of these lysine residues, Lys-313, to isoleucine. Glycan array screening reveals that this amino acid change abolishes binding to oligosaccharides with terminal 6SO4-Gal and enhances binding to oligosaccharides with terminal GlcNAc residues. Structural analysis shows that enhanced binding to GlcNAc may result from Ile-313 packing against the N-acetyl group. The K313I polymorphism is tightly linked to another SNP that results in the change N288D, which reduces affinity for glycan ligands by destabilizing the Ca(2+)-binding site. Langerin with Asp-288 and Ile-313 shows no binding to 6SO4-Gal-terminated glycans and increased binding to GlcNAc-terminated structures, but overall decreased binding to glycans. Altered langerin function in individuals with the linked N288D and K313I polymorphisms may affect susceptibility to infection by microorganisms.

    • Organizational Affiliation: 
    • From the Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom and.

Macromolecule Content 

  • Total Structure Weight: 63.35 kDa 
  • Atom Count: 5,011 
  • Modeled Residue Count: 514 
  • Deposited Residue Count: 544 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
C-type lectin domain family 4 member K
A, B, C, D
136Homo sapiensMutation(s): 2 
Gene Names: CD207, CLEC4K
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UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJ71 (Homo sapiens)
Explore Q9UJ71 
Go to UniProtKB:  Q9UJ71
PHAROS:  Q9UJ71
GTEx:  ENSG00000116031 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJ71
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.229 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.176 (Depositor) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.06α = 90
b = 80.06β = 90
c = 90.17γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
BOSdata collection
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2013-12-04
    Changes: Database references
  • Version 1.2: 2014-01-22
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-11-27
    Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.