5B56

Crystal structure of HIV-1 VPR C-Terminal domain and DIBB-M-Importin-Alpha2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular Mechanism of HIV-1 Vpr for Binding to Importin-alpha

Miyatake, H.Sanjoh, A.Murakami, T.Murakami, H.Matsuda, G.Hagiwara, K.Yokoyama, M.Sato, H.Miyamoto, Y.Dohmae, N.Aida, Y.

(2016) J Mol Biol 428: 2744-2757

  • DOI: 10.1016/j.jmb.2016.05.003
  • Primary Citation of Related Structures:  
    5B56

  • PubMed Abstract: 
  • Viral protein R (Vpr) is an accessory gene product of human immunodeficiency virus type 1 (HIV-1) that plays multiple important roles associated with viral replication. Structural studies using NMR have revealed that Vpr consists of three α-helices a ...

    Viral protein R (Vpr) is an accessory gene product of human immunodeficiency virus type 1 (HIV-1) that plays multiple important roles associated with viral replication. Structural studies using NMR have revealed that Vpr consists of three α-helices and contains flexible N- and C-termini. However, the molecular mechanisms associated with Vpr function have not been elucidated. To investigate Vpr multifunctionality, we performed an X-ray crystallographic study of Vpr complexes containing importin-α, a known Vpr binding partner present in host cells. Elucidation of the crystal structure revealed that the flexible C-terminus changes its conformation to a twisted β-turn via an induced-fit mechanism, enabling binding to a minor nuclear localization signal (NLS) site of importin-α. The Vpr C-terminus can also bind with major NLS sites of importin-α in an extended conformation in different ways. These results, which represent the first reported crystallographic analysis of Vpr, demonstrate the multifunctional aspects that enable Vpr interaction with a variety of cellular proteins.


    Organizational Affiliation

    Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan. Electronic address: aida@riken.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Importin subunit alpha-1A, B460Mus musculusMutation(s): 0 
Gene Names: Kpna2Rch1
Find proteins for P52293 (Mus musculus)
Explore P52293 
Go to UniProtKB:  P52293
NIH Common Fund Data Resources
IMPC  MGI:103561
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein VprC, D, E, F12HIV-1 M:B_89.6Mutation(s): 0 
Gene Names: vpr
Find proteins for Q73369 (Human immunodeficiency virus type 1 group M subtype B (strain 89.6))
Explore Q73369 
Go to UniProtKB:  Q73369
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.021α = 90
b = 81.555β = 97.78
c = 101.545γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-06-29
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Database references, Derived calculations