7CRE

hnRNPK KH3 domain in complex with a ssDNA fragment from the SIRLOIN element


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Nuclear import receptors and hnRNPK mediates nuclear import and stress granule localization of SIRLOIN.

Yao, J.Tu, Y.Shen, C.Zhou, Q.Xiao, H.Jia, D.Sun, Q.

(2021) Cell Mol Life Sci 78: 7617-7633

  • DOI: https://doi.org/10.1007/s00018-021-03992-7
  • Primary Citation of Related Structures:  
    7CRE, 7CRU

  • PubMed Abstract: 

    The majority of lncRNAs and a small fraction of mRNAs localize in the cell nucleus to exert their functions. A SIRLOIN RNA motif was previously reported to drive its nuclear localization by the RNA-binding protein hnRNPK. However, the underlying mechanism remains unclear. Here, we report crystal structures of hnRNPK in complex with SIRLOIN, and with the nuclear import receptor (NIR) Impα1, respectively. The protein hnRNPK bound to SIRLOIN with multiple weak interactions, and interacted Impα1 using an independent high-affinity site. Forming a complex with hnRNPK and Impα1 was essential for the nuclear import and stress granule localization of SIRLOIN in semi-permeabilized cells. Nuclear import of SIRLOIN enhanced with increasing NIR concentrations, but its stress granule localization peaked at a low NIR concentration. Collectively, we propose a mechanism of SIRLOIN localization, in which NIRs functioned as drivers/regulators, and hnRNPK as an adaptor.


  • Organizational Affiliation

    Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu, 610041, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heterogeneous nuclear ribonucleoprotein K76Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P61978 (Homo sapiens)
Explore P61978 
Go to UniProtKB:  P61978
PHAROS:  P61978
GTEx:  ENSG00000165119 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61978
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
ssDNA fragmentB [auth C]16synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.611α = 90
b = 61.611β = 90
c = 144.544γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description