8K9D | pdb_00008k9d

Structure of human Caprin-2 HR1 domain

• PDB DOI: https://doi.org/10.2210/pdb8K9D/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-31 Released: 2024-08-21 
• Deposition Author(s): Song, X.M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.302 (Depositor), 0.301 (DCC) 
• R-Value Work: 
  0.289 (Depositor), 0.289 (DCC) 
• R-Value Observed: 
  0.291 (Depositor) 

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 Biol Chem 300: 107694-107694

• PubMed: 39159816 
• DOI: https://doi.org/10.1016/j.jbc.2024.107694
• Primary Citation 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.

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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.
Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
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; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China. Electronic address: [e-mail].
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. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.55 kDa 
• Atom Count: 931 
• Modeled Residue Count: 123 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caprin-2	A	260	Homo sapiens	Mutation(s): 0  Gene Names: CAPRIN2, C1QDC1, EEG1, KIAA1873, RNG140
UniProt & NIH Common Fund Data Resources
Find proteins for Q6IMN6 (Homo sapiens) Explore Q6IMN6  Go to UniProtKB:  Q6IMN6
PHAROS:  Q6IMN6 GTEx:  ENSG00000110888

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.302 (Depositor), 0.301 (DCC) 
• R-Value Work:  0.289 (Depositor), 0.289 (DCC) 
• R-Value Observed: 0.291 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.852	α = 90
b = 281.903	β = 90
c = 63.449	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31530094
National Natural Science Foundation of China (NSFC)	China	31100532

Revision History  

• 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