4WMQ | pdb_00004wmq

Structure of Human Intelectin-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.164 (Depositor), 0.164 (DCC) 
  • R-Value Work: 
    0.133 (Depositor), 0.135 (DCC) 
  • R-Value Observed: 
    0.135 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4WMQ

This is version 1.5 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: https://doi.org/10.1038/nsmb.3053
  • Primary Citation Related Structures: 
    4WMQ, 4WMY

  • 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 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
    • Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.

Macromolecule Content 

  • Total Structure Weight: 68.76 kDa 
  • Atom Count: 5,215 
  • Modeled Residue Count: 564 
  • Deposited Residue Count: 612 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Intelectin-1
A, B
306Homo sapiensMutation(s): 0 
Gene Names: ITLN1INTLITLNLFRUNQ640/PRO1270
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WWA0 (Homo sapiens)
Explore Q8WWA0 
Go to UniProtKB:  Q8WWA0
PHAROS:  Q8WWA0
GTEx:  ENSG00000179914 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WWA0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.164 (Depositor), 0.164 (DCC) 
  • R-Value Work:  0.133 (Depositor), 0.135 (DCC) 
  • R-Value Observed: 0.135 (Depositor) 
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



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
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary