7VPW | pdb_00007vpw

Crystal structure of Transportin-1 in complex with BAP1 PY-NLS (residues 706-724)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.76 Å
  • R-Value Free: 
    0.258 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7VPW

This is version 1.3 of the entry. See complete history

Literature

Tumor suppressor BAP1 nuclear import is governed by transportin-1.

Yang, T.J.Li, T.N.Huang, R.S.Pan, M.Y.Lin, S.Y.Lin, S.Wu, K.P.Wang, L.H.Hsu, S.D.

(2022) J Cell Biol 221

  • DOI: https://doi.org/10.1083/jcb.202201094
  • Primary Citation Related Structures: 
    7VPW

  • PubMed Abstract: 

    Subcellular localization of the deubiquitinating enzyme BAP1 is deterministic for its tumor suppressor activity. While the monoubiquitination of BAP1 by an atypical E2/E3-conjugated enzyme UBE2O and BAP1 auto-deubiquitination are known to regulate its nuclear localization, the molecular mechanism by which BAP1 is imported into the nucleus has remained elusive. Here, we demonstrated that transportin-1 (TNPO1, also known as Karyopherin β2 or Kapβ2) targets an atypical C-terminal proline-tyrosine nuclear localization signal (PY-NLS) motif of BAP1 and serves as the primary nuclear transporter of BAP1 to achieve its nuclear import. TNPO1 binding dissociates dimeric BAP1 and sequesters the monoubiquitination sites flanking the PY-NLS of BAP1 to counteract the function of UBE2O that retains BAP1 in the cytosol. Our findings shed light on how TNPO1 regulates the nuclear import, self-association, and monoubiquitination of BAP1 pertinent to oncogenesis.


  • Organizational Affiliation
    • Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 100.97 kDa 
  • Atom Count: 6,705 
  • Modeled Residue Count: 841 
  • Deposited Residue Count: 889 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BRCA1-associated protein 1 (BAP1)A [auth B]19Homo sapiensMutation(s): 0 
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q92560 (Homo sapiens)
Explore Q92560 
Go to UniProtKB:  Q92560
PHAROS:  Q92560
GTEx:  ENSG00000163930 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92560
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Transportin-1B [auth A]870Homo sapiensMutation(s): 0 
Gene Names: TNPO1KPNB2MIP1TRN
UniProt & NIH Common Fund Data Resources
Find proteins for Q92973 (Homo sapiens)
Explore Q92973 
Go to UniProtKB:  Q92973
PHAROS:  Q92973
GTEx:  ENSG00000083312 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92973
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.76 Å
  • R-Value Free:  0.258 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.896α = 90
b = 129.688β = 90
c = 170.214γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan110-2113-M-001-050-MY3

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2023-05-03
    Changes: Database references
  • Version 1.2: 2023-05-10
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description