8X0N | pdb_00008x0n

The molecular mechanism of hnRNPA1 recognize TERRA RNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.290 (Depositor), 0.293 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8X0N

This is version 1.2 of the entry. See complete history

Literature

Phase separation of hnRNPA1 and TERRA regulates telomeric stability.

Xu, Z.Liu, Y.Li, F.Yang, Y.Zhang, H.Meng, F.Liu, X.Xie, X.Chen, X.Shi, Y.Zhang, L.

(2025) J Mol Cell Biol 16

  • DOI: https://doi.org/10.1093/jmcb/mjae037
  • Primary Citation Related Structures: 
    8X0N

  • PubMed Abstract: 

    Telomeres are repetitive DNA sequences and associated protein complexes located at the end of chromatin. As a result of the DNA replication ending issue, telomeric DNA shortens during each cell cycle. The shelterin protein complex caps telomeric ends and forms a high-order protein-DNA structure to protect telomeric DNA. The stability of telomeres is critical for cellular function and is related to the progression of many human diseases. Telomeric repeat-containing RNA (TERRA) is a noncoding RNA transcribed from telomeric DNA regions. TERRA plays an essential role in regulating and maintaining the stability of telomeres. Heterogeneous nuclear ribonucleoproteins (hnRNPs) are RNA-binding proteins associated with complex and diverse biological processes. HnRNPA1 can recognize both TERRA and telomeric DNA. Previous research reported that hnRNPA1, TERRA, and POT1, a component of the shelterin complex, worked coordinately and displaced replication protein A from telomeric ssDNA after DNA replication, promoting telomere capping to preserve genomic integrity. However, the detailed molecular mechanism has remained unclear for over twenty years. Our study revealed the molecular structure through which the hnRNPA1 UP1 domain interacts with TERRA. Through structural analysis, we identified critical residues on the interacting surface between UP1 and TERRA. Furthermore, we proved that nucleic acids significantly increase the phase separation ability of hnRNPA1 and disrupting the UP1-TERRA interaction extraordinarily affects hnRNPA1 droplet formation both in vitro and in vivo. Taken together, these data revealed the molecular mechanism of the droplet formation of hnRNPA1 and TERRA and the possible function of the droplets for maintaining genomic stability.


  • Organizational Affiliation
    • Center for Advanced Interdisciplinary Science and Biomedicine of IHM; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; Hefei National Research Center for Cross-disciplinary Science; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.

Macromolecule Content 

  • Total Structure Weight: 27.04 kDa 
  • Atom Count: 1,708 
  • Modeled Residue Count: 193 
  • Deposited Residue Count: 214 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heterogeneous nuclear ribonucleoprotein A1202Homo sapiensMutation(s): 0 
Gene Names: HNRNPA1
UniProt & NIH Common Fund Data Resources
Find proteins for P09651 (Homo sapiens)
Explore P09651 
Go to UniProtKB:  P09651
PHAROS:  P09651
GTEx:  ENSG00000135486 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09651
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*G)-3')12Homo sapiens
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.290 (Depositor), 0.293 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.298α = 90
b = 101.298β = 90
c = 55.339γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32090040

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references
  • Version 1.2: 2025-05-07
    Changes: Database references