8JAH

Crystal structure of human CLEC12A C-type lectin domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanistic insights into the C-type lectin receptor CLEC12A-mediated immune recognition of monosodium urate crystal.

Tang, H.Xiao, Y.Qian, L.Wang, Z.Lu, M.Yao, N.Zhou, T.Tian, F.Cao, L.Zheng, P.Dong, X.

(2024) J Biol Chem 300: 105765-105765

  • DOI: https://doi.org/10.1016/j.jbc.2024.105765
  • Primary Citation of Related Structures:  
    8JAH

  • PubMed Abstract: 

    CLEC12A, a member of the C-type lectin receptor family involved in immune homeostasis, recognizes MSU crystals released from dying cells. However, the molecular mechanism underlying the CLEC12A-mediated recognition of MSU crystals remains unclear. Herein, we reported the crystal structure of the human CLEC12A-C-type lectin-like domain (CTLD) and identified a unique "basic patch" site on CLEC12A-CTLD that is necessary for the binding of MSU crystals. Meanwhile, we determined the interaction strength between CLEC12A-CTLD and MSU crystals using single-molecule force spectroscopy. Furthermore, we found that CLEC12A clusters at the cell membrane and seems to serve as an internalizing receptor of MSU crystals. Altogether, these findings provide mechanistic insights for understanding the molecular mechanisms underlying the interplay between CLEC12A and MSU crystals.


  • Organizational Affiliation

    State Key Laboratory of Pharmaceutical Biotechnology, Department of Biochemistry, School of Life Sciences, Nanjing University, Nanjing, China; Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, China. Electronic address: tanghua@nju.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-type lectin domain family 12 member A
A, B
122Homo sapiensMutation(s): 0 
Gene Names: CLEC12ACLL1DCAL2MICL
UniProt & NIH Common Fund Data Resources
Find proteins for Q5QGZ9 (Homo sapiens)
Explore Q5QGZ9 
Go to UniProtKB:  Q5QGZ9
PHAROS:  Q5QGZ9
GTEx:  ENSG00000172322 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5QGZ9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.012α = 90
b = 50.012β = 90
c = 367.627γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171254
National Natural Science Foundation of China (NSFC)China32201007

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Database references