1PD3 | pdb_00001pd3

Influenza A NEP M1-binding domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.244 (Depositor) 
  • R-Value Work: 
    0.176 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

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 the M1 protein-binding domain of the influenza A virus nuclear export protein (NEP/NS2).

Akarsu, H., Burmeister, W.P., Petosa, C., Petit, I., Muller, C.W., Ruigrok, R.W., Baudin, F.

(2003) EMBO J 22: 4646-4655

  • DOI: https://doi.org/10.1093/emboj/cdg449
  • Primary Citation Related Structures: 
    1PD3

  • PubMed Abstract: 

    During influenza virus infection, viral ribonucleoproteins (vRNPs) are replicated in the nucleus and must be exported to the cytoplasm before assembling into mature viral particles. Nuclear export is mediated by the cellular protein Crm1 and putatively by the viral protein NEP/NS2. Proteolytic cleavage of NEP defines an N-terminal domain which mediates RanGTP-dependent binding to Crm1 and a C-terminal domain which binds to the viral matrix protein M1. The 2.6 A crystal structure of the C-terminal domain reveals an amphipathic helical hairpin which dimerizes as a four-helix bundle. The NEP-M1 interaction involves two critical epitopes: an exposed tryptophan (Trp78) surrounded by a cluster of glutamate residues on NEP, and the basic nuclear localization signal (NLS) of M1. Implications for vRNP export are discussed.

    • Organizational Affiliation: 
    • EMBL Grenoble Outstation, BP 181, 38042 Grenoble cedex 9, France.

Macromolecule Content 

  • Total Structure Weight: 14.48 kDa 
  • Atom Count: 948 
  • Modeled Residue Count: 108 
  • Deposited Residue Count: 116 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nonstructural protein NS2
A, B
58Influenza A virusMutation(s): 0 
Gene Names: NS2
UniProt
Find proteins for P03508 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Explore P03508 
Go to UniProtKB:  P03508
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03508
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.244 (Depositor) 
  • R-Value Work:  0.176 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.691α = 90
b = 82.691β = 90
c = 61.111γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2003-12-16 
    • Deposition Author(s): Baudin, F.

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references