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- PDB-7p3m: Solution structures of HIV-1 and SIVmac p6 and their interaction ... -

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Basic information

Entry
Database: PDB / ID: 7p3m
TitleSolution structures of HIV-1 and SIVmac p6 and their interaction with accessory proteins Vpr and Vpx in the presence of DPC micelles
ComponentsGag polyprotein
KeywordsVIRAL PROTEIN / siv / p6
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / host cell plasma membrane / structural molecule activity / RNA binding / zinc ion binding / membrane
Similarity search - Function
: / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal ...: / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesSimian immunodeficiency virus
MethodSOLUTION NMR / torsion angle dynamics
AuthorsWang, X. / Nonin-Lecomte, S. / Bouaziz, S.
CitationJournal: To Be Published
Title: Solution structures of HIV-1 and SIVmac p6 and their interaction with accessory proteins Vpr and Vpx in the presence of DPC micelles
Authors: Wang, X.
History
DepositionJul 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Structure summary / Category: audit_author / chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gag polyprotein


Theoretical massNumber of molelcules
Total (without water)1,5371
Polymers1,5371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Gag polyprotein / Pr55Gag


Mass: 1536.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian immunodeficiency virus (isolate K6W)
Strain: isolate K6W / Gene: gag / Production host: Synthecium (invertebrata) / References: UniProt: P05893

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution / Contents: 1.0 mM unlabeled SIVmac p6, 90% H2O/10% D2O / Label: unlebeled_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: SIVmac p6 / Isotopic labeling: unlabeled
Sample conditionsIonic strength: 50 mM / Label: condition_1 / pH: 4 / Pressure: 1 atm / Temperature: 323 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz / Details: cryo-probe

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 2 / Details: restraints, 172 distance retraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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