4WMQ

Structure of Human Intelectin-1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.135 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Recognition of microbial glycans by human intelectin-1.

Wesener, D.A., Wangkanont, K., McBride, R., Song, X., Kraft, M.B., Hodges, H.L., Zarling, L.C., Splain, R.A., Smith, D.F., Cummings, R.D., Paulson, J.C., Forest, K.T., Kiessling, L.L.

(2015) Nat Struct Mol Biol 22: 603-610

  • DOI: 10.1038/nsmb.3053
  • Primary Citation of Related Structures:  
    4WMY, 4WMQ

  • PubMed Abstract: 

    • The glycans displayed on mammalian cells can differ markedly from those on microbes. Such differences could, in principle, be 'read' by carbohydrate-binding proteins, or lectins. We used glycan microarrays to show that human intelectin-1 (hIntL-1) does not bind known human glycan epitopes but does interact with multiple glycan epitopes found exclusively on microbes: β-linked D-galactofuranose (β-Galf), D-phosphoglycerol-modified glycans, heptoses, D-glycero-D-talo-oct-2-ulosonic acid (KO) and 3-deoxy-D-manno-oct-2-ulosonic acid (KDO) ...

    The glycans displayed on mammalian cells can differ markedly from those on microbes. Such differences could, in principle, be 'read' by carbohydrate-binding proteins, or lectins. We used glycan microarrays to show that human intelectin-1 (hIntL-1) does not bind known human glycan epitopes but does interact with multiple glycan epitopes found exclusively on microbes: β-linked D-galactofuranose (β-Galf), D-phosphoglycerol-modified glycans, heptoses, D-glycero-D-talo-oct-2-ulosonic acid (KO) and 3-deoxy-D-manno-oct-2-ulosonic acid (KDO). The 1.6-Å-resolution crystal structure of hIntL-1 complexed with β-Galf revealed that hIntL-1 uses a bound calcium ion to coordinate terminal exocyclic 1,2-diols. N-acetylneuraminic acid (Neu5Ac), a sialic acid widespread in human glycans, has an exocyclic 1,2-diol but does not bind hIntL-1, probably owing to unfavorable steric and electronic effects. hIntL-1 marks only Streptococcus pneumoniae serotypes that display surface glycans with terminal 1,2-diol groups. This ligand selectivity suggests that hIntL-1 functions in microbial surveillance.

    Organizational Affiliation: 

    1] Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA. [2] Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Intelectin-1 A, B306Homo sapiensMutation(s): 0 
Gene Names: ITLN1, INTL, ITLN, LFR, UNQ640/PRO1270
Find proteins for Q8WWA0 (Homo sapiens)
Explore Q8WWA0 
Go to UniProtKB:  Q8WWA0
NIH Common Fund Data Resources
PHAROS:  Q8WWA0
GTEx:  ENSG00000179914
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.135 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.45α = 90
b = 118.45β = 90
c = 118.45γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Database references
  • Version 1.2: 2015-08-19
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2021-03-24
    Changes: Derived calculations, Source and taxonomy