4YLI

CL-K1 trimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 2.1 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.


  • Organizational Affiliation

    Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, UK. pcem1@leicester.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Collectin-11
A, B, C, D, E
A, B, C, D, E, F
155Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
FA [auth E]
GA [auth E]
K [auth A]
AA [auth D],
BA [auth D],
FA [auth E],
GA [auth E],
K [auth A],
KA [auth F],
L [auth A],
LA [auth F],
P [auth B],
Q [auth B],
R [auth B],
V [auth C],
W [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth E]
DA [auth E]
EA [auth E]
G [auth A]
H [auth A]
CA [auth E],
DA [auth E],
EA [auth E],
G [auth A],
H [auth A],
HA [auth F],
I [auth A],
IA [auth F],
JA [auth F],
M [auth B],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
U [auth C],
X [auth D],
Y [auth D],
Z [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.99α = 90
b = 107.59β = 91.49
c = 77.82γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
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: Advisory, Atomic model, Author supporting evidence, Derived calculations
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description