8CMK | pdb_00008cmk

Transportin-3 TNPO3 in complex with RSY region of CIRBP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 
    0.317 (Depositor), 0.320 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.240 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural basis of phosphorylation-independent nuclear import of CIRBP by TNPO3.

Zhou, Q.Sagmeister, T.Hutten, S.Bourgeois, B.Pavkov-Keller, T.Dormann, D.Madl, T.

(2025) Nat Commun 16: 4456-4456

  • DOI: https://doi.org/10.1038/s41467-025-59802-2
  • Primary Citation of Related Structures:  
    8CMK

  • PubMed Abstract: 

    Transportin 3 (TNPO3) is a nuclear import receptor known for its broad substrate specificity, often recognizing arginine-serine (SR/RS) repeat-rich nuclear localization signals (NLS) in SRSF proteins. While serine phosphorylation or glutamate presence has been associated with these NLSs, recent proteomic studies identified TNPO3 cargoes lacking SR/RS repeats. One such example is the cold-inducible RNA-binding protein (CIRBP), which contains a non-classical RSY-NLS. Using X-ray crystallography, here we investigate the TNPO3-CIRBP interaction and find that tyrosines within the RSY-NLS play a key role in binding, independent of phosphorylation. Surprisingly, serine and tyrosine phosphorylation in CIRBP's NLS inhibits TNPO3 binding, suggesting a regulatory mechanism for nuclear import. Our study reveals a non-conventional nuclear import mechanism mediated by TNPO3, which may extend to other known or yet undiscovered TNPO3 cargoes.


  • Organizational Affiliation
    • Research Unit Integrative Structural Biology, Medicinal Chemistry, Otto Loewi Research Center, Medical University of Graz, Graz, Austria.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transportin-3
A, B
923Homo sapiensMutation(s): 1 
Gene Names: TNPO3IPO12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5L0 (Homo sapiens)
Explore Q9Y5L0 
Go to UniProtKB:  Q9Y5L0
PHAROS:  Q9Y5L0
GTEx:  ENSG00000064419 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5L0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cold-inducible RNA-binding protein
C, D, E
35Homo sapiensMutation(s): 0 
Gene Names: CIRBPA18HNRNPCIRP
UniProt & NIH Common Fund Data Resources
Find proteins for Q14011 (Homo sapiens)
Explore Q14011 
Go to UniProtKB:  Q14011
PHAROS:  Q14011
GTEx:  ENSG00000099622 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14011
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free:  0.317 (Depositor), 0.320 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.240 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.526α = 90
b = 101.805β = 111.128
c = 114.133γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Research Promotion AgencyAustria864690
Austrian Research Promotion AgencyAustria870454
Austrian Science FundAustriaP28854
Austrian Science FundAustriaI3792
Austrian Science FundAustriaDOC-130
Austrian Science FundAustriaW1226

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Database references, Structure summary