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- PDB-1u57: NMR structure of the (345-392)Gag sequence from HIV-1 -

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Basic information

Entry
Database: PDB / ID: 1u57
TitleNMR structure of the (345-392)Gag sequence from HIV-1
ComponentsGag polyproteinGroup-specific antigen
KeywordsVIRAL PROTEIN / Gag polyprotein / particle assembly / p2 / HIV-1
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane
Similarity search - Function
Single helix bin / Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal ...Single helix bin / Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing
AuthorsMorellet, N. / Druillennec, S. / Lenoir, C. / Bouaziz, S. / Roques, B.P.
CitationJournal: Protein Sci. / Year: 2005
Title: Helical structure determined by NMR of the HIV-1 (345-392)Gag sequence, surrounding p2: Implications for particle assembly and RNA packaging
Authors: Morellet, N. / Druillennec, S. / Lenoir, C. / Bouaziz, S. / Roques, B.P.
History
DepositionJul 27, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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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)5,2561
Polymers5,2561
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 100structures with acceptable covalent geometry
RepresentativeModel #2fewest violations

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Components

#1: Protein/peptide Gag polyprotein / Group-specific antigen / HIV-1


Mass: 5256.142 Da / Num. of mol.: 1 / Fragment: residues 1-48 / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: lw12.3 isolate / References: UniProt: Q70622

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1413D NOESY-NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 1mM (211-231)CA-p2-(1-13)NCp7 peptide, 70% H2O, 30% TFE pH 3.5
Solvent system: 70% H2O, 30% TFE
Sample conditionspH: 3.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR3Brukercollection
UXNMR3brukerprocessing
Discover2.9.7Accelrysrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 478 NOE-derived, distance constraints and 92 dihedral angle restraints
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 100 / Conformers submitted total number: 19

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