4JLQ | pdb_00004jlq

Crystal structure of human Karyopherin-beta2 bound to the PY-NLS of Saccharomyces cerevisiae NAB2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 
    0.237 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.184 (Depositor) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of human Karyopherin beta 2 bound to the PY-NLS of Saccharomyces cerevisiae Nab2.

Soniat, M.Sampathkumar, P.Collett, G.Gizzi, A.S.Banu, R.N.Bhosle, R.C.Chamala, S.Chowdhury, S.Fiser, A.Glenn, A.S.Hammonds, J.Hillerich, B.Khafizov, K.Love, J.D.Matikainen, B.Seidel, R.D.Toro, R.Rajesh Kumar, P.Bonanno, J.B.Chook, Y.M.Almo, S.C.

(2013) J Struct Funct Genomics 14: 31-35

  • DOI: https://doi.org/10.1007/s10969-013-9150-1
  • Primary Citation Related Structures: 
    4JLQ

  • PubMed Abstract: 

    Import-Karyopherin or Importin proteins bind nuclear localization signals (NLSs) to mediate the import of proteins into the cell nucleus. Karyopherin β2 or Kapβ2, also known as Transportin, is a member of this transporter family responsible for the import of numerous RNA binding proteins. Kapβ2 recognizes a targeting signal termed the PY-NLS that lies within its cargos to target them through the nuclear pore complex. The recognition of PY-NLS by Kapβ2 is conserved throughout eukaryotes. Kap104, the Kapβ2 homolog in Saccharomyces cerevisiae, recognizes PY-NLSs in cargos Nab2, Hrp1, and Tfg2. We have determined the crystal structure of Kapβ2 bound to the PY-NLS of the mRNA processing protein Nab2 at 3.05-Å resolution. A seven-residue segment of the PY-NLS of Nab2 is observed to bind Kapβ2 in an extended conformation and occupies the same PY-NLS binding site observed in other Kapβ2·PY-NLS structures.


  • Organizational Affiliation
    • Department of Pharmacology, University of Texas Southwestern, Dallas, TX 75390, USA. michael.soniat@utsouthwestern.edu

Macromolecule Content 

  • Total Structure Weight: 100.79 kDa 
  • Atom Count: 6,733 
  • Modeled Residue Count: 847 
  • Deposited Residue Count: 892 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transportin-1854Homo sapiensMutation(s): 0 
Gene Names: KPNB2MIP1TNPO1TRN
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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear polyadenylated RNA-binding protein NAB238Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NAB2YGL122C
UniProt
Find proteins for P32505 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32505 
Go to UniProtKB:  P32505
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32505
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free:  0.237 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.184 (Depositor) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.234α = 90
b = 172.383β = 90
c = 68.443γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description