4JLQ

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 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1007/s10969-013-9150-1
  • Primary Citation of 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 ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transportin-1A854Homo sapiensMutation(s): 0 
Gene Names: KPNB2MIP1TNPO1TRN
Find proteins for Q92973 (Homo sapiens)
Explore Q92973 
Go to UniProtKB:  Q92973
NIH Common Fund Data Resources
PHAROS  Q92973
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear polyadenylated RNA-binding protein NAB2B38Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NAB2YGL122C
Find proteins for P32505 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32505 
Go to UniProtKB:  P32505
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • 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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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