8K9D | pdb_00008k9d

Structure of human Caprin-2 HR1 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.302 (Depositor), 0.310 (DCC) 
  • R-Value Work: 
    0.289 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 
    0.291 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the Caprin-2 HR1 domain in canonical Wnt signaling.

Su, C.Zhong, Y.Zhou, Z.Li, Y.Jia, Y.Xie, S.Zhao, J.Miao, H.Luo, H.Li, Z.Shi, Z.Li, L.Song, X.

(2024) J Biological Chem 300: 107694-107694

  • DOI: https://doi.org/10.1016/j.jbc.2024.107694
  • Primary Citation of Related Structures:  
    8K9D

  • PubMed Abstract: 

    The canonical Wnt signaling pathway plays crucial roles in cell fate decisions as well as in pathogenesis of various diseases. Previously, we reported Caprin-2 as a new regulator of canonical Wnt signaling through a mechanism of facilitating LRP5/6 phosphorylation. Here, we resolved the crystal structure of the N-terminal homologous region 1 (HR1) domain of human Caprin-2. HR1 domain is so far only observed in Caprin-2 and its homologous protein Caprin-1, and the function of this domain remains largely mysterious. Here, the structure showed that HR1 domain of human Caprin-2 forms a homo-dimer and exhibits an overall structure roughly resembling the appearance of a pair of scissors. Moreover, we found that residues R200 and R201, which located at a basic cluster within the N-terminal "blades" region, are critical for Caprin-2's localization to the plasma membrane. In line with this, mutations targeting these two residues decrease Caprin-2's activity in the canonical Wnt signaling. Overall, we characterized a previously unknown "scissors"-like structure of the full-length HR1 domain and revealed its function in mediating Caprin-2's localization to the plasma membrane.


  • Organizational Affiliation
    • Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Caprin-2260Homo sapiensMutation(s): 0 
Gene Names: CAPRIN2C1QDC1EEG1KIAA1873RNG140
UniProt & NIH Common Fund Data Resources
Find proteins for Q6IMN6 (Homo sapiens)
Explore Q6IMN6 
Go to UniProtKB:  Q6IMN6
PHAROS:  Q6IMN6
GTEx:  ENSG00000110888 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IMN6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.302 (Depositor), 0.310 (DCC) 
  • R-Value Work:  0.289 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 0.291 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.852α = 90
b = 281.903β = 90
c = 63.449γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2024-08-21 
  • Deposition Author(s): Song, X.M.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31530094
National Natural Science Foundation of China (NSFC)China31100532

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-21
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary
  • Version 1.2: 2025-03-05
    Changes: Database references