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- PDB-1dsk: NMR SOLUTION STRUCTURE OF VPR59_86, 20 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1dsk
TitleNMR SOLUTION STRUCTURE OF VPR59_86, 20 STRUCTURES
ComponentsVPR PROTEIN
KeywordsVIRAL PEPTIDE / POLYPEPTIDE
Function / homology
Function and homology information


symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont-mediated activation of host apoptosis / protein homooligomerization / virion component / viral penetration into host nucleus / host cell / monoatomic ion transmembrane transport / host extracellular space / DNA-templated transcription / regulation of DNA-templated transcription ...symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont-mediated activation of host apoptosis / protein homooligomerization / virion component / viral penetration into host nucleus / host cell / monoatomic ion transmembrane transport / host extracellular space / DNA-templated transcription / regulation of DNA-templated transcription / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Retroviral VpR/VpX protein / VPR/VPX protein
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR
AuthorsYao, S. / Torres, A.M. / Azad, A.A. / Macreadie, I.G. / Norton, R.S.
Citation
Journal: J. Pept. Sci. / Year: 1998
Title: Solution structure of peptides from HIV-1 Vpr protein that cause membrane permeabilization and growth arrest.
Authors: Yao, S. / Torres, A.M. / Azad, A.A. / Macreadie, I.G. / Norton, R.S.
#1: Journal: Gene / Year: 1996
Title: Characterization of a leucine-zipper-like domain in Vpr protein of human immunodeficiency virus type 1.
Authors: Wang, L. / Mukherjee, S. / Narayan, O. / Zhao, L.J.
#2: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 1995
Title: A domain of human immunodeficiency virus type 1 Vpr containing repeated H(S/F)RIG amino acid motifs causes cell growth arrest and structural defects.
Authors: Macreadie, I.G. / Castelli, L.A. / Hewish, D.R. / Kirkpatrick, A. / Ward, A.C. / Azad, A.A.
History
DepositionOct 23, 1997Processing site: BNL
Revision 1.0Jul 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2017Group: Database references / Derived calculations / Other
Category: citation / pdbx_database_status ...citation / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_database_status.process_site
Revision 1.4Apr 10, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VPR PROTEIN


Theoretical massNumber of molelcules
Total (without water)3,3531
Polymers3,3531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3130 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

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Components

#1: Protein/peptide VPR PROTEIN


Mass: 3353.068 Da / Num. of mol.: 1 / Fragment: RESIDUES 59 - 86
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / References: UniProt: P12520

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 3.3 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 20

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