7XHG | pdb_00007xhg

Crystal structure of the NTF2L domain of human G3BP1 in complex with the Caprin-1 derived peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 
    0.275 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7XHG

This is version 1.1 of the entry. See complete history

Literature

Yin and yang regulation of stress granules by Caprin-1.

Song, D.Kuang, L.Yang, L.Wang, L.Li, H.Li, X.Zhu, Z.Shi, C.Zhu, H.Gong, W.

(2022) Proc Natl Acad Sci U S A 119: e2207975119-e2207975119

  • DOI: https://doi.org/10.1073/pnas.2207975119
  • Primary Citation Related Structures: 
    7XHF, 7XHG

  • PubMed Abstract: 

    Stress granules (SGs) are cytoplasmic biomolecular condensates containing proteins and RNAs in response to stress. Ras-GTPase-activating protein binding protein 1 (G3BP1) is a core SG protein. Caprin-1 and ubiquitin specific peptidase 10 (USP10) interact with G3BP1, facilitating and suppressing SG formation, respectively. The crystal structures of the nuclear transport factor 2-like (NTF2L) domain of G3BP1 in complex with the G3BP1-interacting motif (GIM) of Caprin-1 and USP10 show that both GIMs bind to the same hydrophobic pocket of G3BP1. Moreover, both GIMs suppressed the liquid-liquid phase separation (LLPS) of G3BP1, suggesting that Caprin-1 likely facilitates SG formation via other mechanisms. Thus, we dissected various domains of Caprin-1 and investigated their role in LLPS in vitro and SG formation in cells. The C-terminal domain of Caprin-1 underwent spontaneous LLPS, whereas the N-terminal domain and GIM of Caprin-1 suppressed LLPS of G3BP1. The opposing effect of the N- and C-terminal domains of Caprin-1 on SG formation were demonstrated in cells with or without the endogenous Caprin-1. We propose that the N- and C-terminal domains of Caprin-1 regulate SG formation in a "yin and yang" fashion, mediating the dynamic and reversible assembly of SGs.


  • Organizational Affiliation
    • School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China.

Macromolecule Content 

  • Total Structure Weight: 67.28 kDa 
  • Atom Count: 4,526 
  • Modeled Residue Count: 553 
  • Deposited Residue Count: 586 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ras GTPase-activating protein-binding protein 1
A, B, C, D
139Homo sapiensMutation(s): 0 
Gene Names: G3BP1G3BP
EC: 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13283 (Homo sapiens)
Explore Q13283 
Go to UniProtKB:  Q13283
PHAROS:  Q13283
GTEx:  ENSG00000145907 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13283
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Caprin-1(369-378)E [auth F],
F [auth G],
G [auth E]
10Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q14444 (Homo sapiens)
Explore Q14444 
Go to UniProtKB:  Q14444
PHAROS:  Q14444
GTEx:  ENSG00000135387 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14444
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free:  0.275 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.669α = 90
b = 171.761β = 99.82
c = 42.968γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-18
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description