5X8N | pdb_00005x8n

Crystal structure of mouse importin-alpha1 bound to the nuclear localization signal of Epstein-Barr virus EBNA-LP protein

• PDB DOI: https://doi.org/10.2210/pdb5X8N/pdb

• Classification: PROTEIN TRANSPORT/TRANSCRIPTION
• Organism(s): Mus musculus, Human herpesvirus 4 strain B95-8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-03 Released: 2017-04-19 
• Deposition Author(s): Nakada, R., Matsuura, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.210 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of importin-alpha bound to the nuclear localization signal of Epstein-Barr virus EBNA-LP protein

Nakada, R., Matsuura, Y.

(2017) Protein Sci 26: 1231-1235

• PubMed: 28383161 
• DOI: https://doi.org/10.1002/pro.3173
• Primary Citation Related Structures: 
  5X8N


• PubMed Abstract: 
  

  Epstein-Barr virus EBNA-LP protein is a transcriptional coactivator of EBNA2. Efficient nuclear localization of EBNA-LP is essential for cooperation with EBNA2. Here, we report the crystal structure of the nuclear import adaptor importin-α1 bound to the nuclear localization signal (NLS) of EBNA-LP that shows EBNA-LP residues 44-RRVRRR-49 binding to the major NLS-binding site at the P0-P5 positions. In contrast to previously characterized classical NLSs that invariably have a basic residue [either lysine (in the vast majority of cases) or arginine] at the P2 position, the EBNA-LP NLS is unique in that it has valine at the P2 position. The loss of the critical P2 lysine (or arginine) is compensated by arginine at the P0 position in the EBNA-LP NLS.

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Organizational Affiliation: 
• Division of Biological Science, Graduate School of Science, Nagoya University, Japan.
Structural Biology Research Center, Graduate School of Science, Nagoya University, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 52.59 kDa 
• Atom Count: 3,439 
• Modeled Residue Count: 433 
• Deposited Residue Count: 482 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Importin subunit alpha-1	A	460	Mus musculus	Mutation(s): 0  Gene Names: Kpna2, Rch1
UniProt & NIH Common Fund Data Resources
Find proteins for P52293 (Mus musculus) Explore P52293  Go to UniProtKB:  P52293
IMPC:  MGI:103561

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Epstein-Barr nuclear antigen leader protein	B	22	Human herpesvirus 4 strain B95-8	Mutation(s): 0
UniProt
Find proteins for Q8AZK7 (Epstein-Barr virus (strain B95-8)) Explore Q8AZK7  Go to UniProtKB:  Q8AZK7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.210 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.27	α = 90
b = 90.29	β = 90
c = 98.17	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data collection
Aimless	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
Aimless	data processing
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-19 
Deposition Author(s): Nakada, R., Matsuura, Y.

Revision History  

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description