Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 100790.23 
• Atom Count: 6733 
• Residue Count: 892 
• Unique protein chains: 2

4JLQ

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

• DOI: 10.2210/pdb4JLQ/pdb
• Entry 4JLQ supersedes 4H1K

• Classification: TRANSPORT PROTEIN
• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2013-03-12 Released: 2013-04-03 
• Deposition Author(s): Sampathkumar, P., Gizzi, A., Rout, M.P., Chook, Y.M., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Nucleocytoplasmic Transport: a Target for Cellular Control (NPCXstals)

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Experimental Data Snapshot

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

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.Genom. 14: 31-35

• PubMed: 23535894 
• DOI: 10.1007/s10969-013-9150-1


• 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.

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Organizational Affiliation: 

Department of Pharmacology, University of Texas Southwestern, Dallas, TX 75390, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Transportin-1	A	854	Homo sapiens	Mutation(s): 0  Gene Names: TNPO1 (KPNB2, MIP1, TRN)
Find proteins for Q92973 (Homo sapiens) Go to Gene View: TNPO1 Go to UniProtKB:  Q92973

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Nuclear polyadenylated RNA-binding protein NAB2	B	38	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NAB2
Find proteins for P32505 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: NAB2 Go to UniProtKB:  P32505

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.237 
• R-Value Work: 0.184 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 132.234	α = 90.00
b = 172.383	β = 90.00
c = 68.443	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
HKL-3000	data reduction
SCALEPACK	data scaling
REFMAC	refinement
CBASS	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-03-12 
• Released Date: 2013-04-03 
• Deposition Author(s): Sampathkumar, P., Gizzi, A., Rout, M.P., Chook, Y.M., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Nucleocytoplasmic Transport: a Target for Cellular Control (NPCXstals)
• This entry supersedes: 4H1K

Revision History 

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