7CRU | pdb_00007cru

hnRNPK NLS in complex with Importin alpha 1 (KPNA2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.240 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 105.18 kDa 
  • Atom Count: 6,959 
  • Modeled Residue Count: 893 
  • Deposited Residue Count: 960 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heterogeneous nuclear ribonucleoprotein KA [auth B],
C [auth D]
23Homo sapiensMutation(s): 0 
Gene Names: HNRNPKHNRPK
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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Importin subunit alpha-1B [auth A],
D [auth C]
457Homo sapiensMutation(s): 0 
Gene Names: KPNA2RCH1SRP1
UniProt & NIH Common Fund Data Resources
Find proteins for P52292 (Homo sapiens)
Explore P52292 
Go to UniProtKB:  P52292
PHAROS:  P52292
GTEx:  ENSG00000182481 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52292
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.240 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.792α = 90
b = 83.317β = 98.24
c = 101.372γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description