4YMD

CL-K1 trimer bound to man(alpha1-2)man


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 3.2 of the entry. See complete history


Literature

Molecular basis of sugar recognition by collectin-K1 and the effects of mutations associated with 3MC syndrome.

Girija, U.V.Furze, C.M.Gingras, A.R.Yoshizaki, T.Ohtani, K.Marshall, J.E.Wallis, A.K.Schwaeble, W.J.El-Mezgueldi, M.Mitchell, D.A.Moody, P.C.Wakamiya, N.Wallis, R.

(2015) BMC Biol 13: 27-27

  • DOI: https://doi.org/10.1186/s12915-015-0136-2
  • Primary Citation of Related Structures:  
    4YLI, 4YMD

  • PubMed Abstract: 

    Collectin-K1 (CL-K1, or CL-11) is a multifunctional Ca(2+)-dependent lectin with roles in innate immunity, apoptosis and embryogenesis. It binds to carbohydrates on pathogens to activate the lectin pathway of complement and together with its associated serine protease MASP-3 serves as a guidance cue for neural crest development. High serum levels are associated with disseminated intravascular coagulation, where spontaneous clotting can lead to multiple organ failure. Autosomal mutations in the CL-K1 or MASP-3 genes cause a developmental disorder called 3MC (Carnevale, Mingarelli, Malpuech and Michels) syndrome, characterised by facial, genital, renal and limb abnormalities. One of these mutations (Gly(204)Ser in the CL-K1 gene) is associated with undetectable levels of protein in the serum of affected individuals. In this study, we show that CL-K1 primarily targets a subset of high-mannose oligosaccharides present on both self- and non-self structures, and provide the structural basis for its ligand specificity. We also demonstrate that three disease-associated mutations prevent secretion of CL-K1 from mammalian cells, accounting for the protein deficiency observed in patients. Interestingly, none of the mutations prevent folding or oligomerization of recombinant fragments containing the mutations in vitro. Instead, they prevent Ca(2+) binding by the carbohydrate-recognition domains of CL-K1. We propose that failure to bind Ca(2+) during biosynthesis leads to structural defects that prevent secretion of CL-K1, thus providing a molecular explanation of the genetic disorder. We have established the sugar specificity of CL-K1 and demonstrated that it targets high-mannose oligosaccharides on self- and non-self structures via an extended binding site which recognises the terminal two mannose residues of the carbohydrate ligand. We have also shown that mutations associated with a rare developmental disorder called 3MC syndrome prevent the secretion of CL-K1, probably as a result of structural defects caused by disruption of Ca(2+) binding during biosynthesis.


  • Organizational Affiliation

    Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, LE1 9HN, UK. uvg1@leicester.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Collectin-11155Homo sapiensMutation(s): 0 
Gene Names: COLEC11UNQ596/PRO1182
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BWP8 (Homo sapiens)
Explore Q9BWP8 
Go to UniProtKB:  Q9BWP8
PHAROS:  Q9BWP8
GTEx:  ENSG00000118004 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BWP8
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose
G, H, I, J
2N/A
Glycosylation Resources
GlyTouCan:  G53402KW
GlyCosmos:  G53402KW
GlyGen:  G53402KW
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C]
EA [auth C]
IA [auth E]
N [auth A]
R [auth B]
AA [auth C],
EA [auth C],
IA [auth E],
N [auth A],
R [auth B],
V [auth D],
Z [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
DA [auth C]
FA [auth E]
GA [auth E]
BA [auth C],
CA [auth C],
DA [auth C],
FA [auth E],
GA [auth E],
HA [auth E],
K [auth A],
L [auth A],
M [auth A],
O [auth B],
P [auth B],
Q [auth B],
S [auth D],
T [auth D],
U [auth D],
W [auth F],
X [auth F],
Y [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.85α = 90
b = 106.65β = 92.17
c = 78.39γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomG1000191/1

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-05-13
    Changes: Database references
  • Version 2.0: 2017-08-30
    Changes: Atomic model, Author supporting evidence, Derived calculations
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 3.2: 2024-10-16
    Changes: Structure summary