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- PDB-1gwp: STRUCTURE OF THE N-TERMINAL DOMAIN OF THE MATURE HIV-1 CAPSID PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1gwp
TitleSTRUCTURE OF THE N-TERMINAL DOMAIN OF THE MATURE HIV-1 CAPSID PROTEIN
ComponentsGAG POLYPROTEIN
KeywordsVIRAL PROTEIN / HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 CAPSID PROTEIN / AMIMO-TERMINAL CORE DOMAIN / HIV-1 CA-151 / VIRUS CAPSID PROTEIN / VIRUS MATURATION
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding ...viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane
Similarity search - Function
Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / : / 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 ...Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / : / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS TYPE 1
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTang, C. / Gitti, R.K. / Lee, B.M. / Walker, J. / Summers, M.F. / Yoo, S. / Sundquist, W.I.
Citation
Journal: Nat.Struct.Biol. / Year: 2002
Title: Structure of the N-Terminal 283-Residue Fragment of the Immature HIV-1 Gag Polyprotein
Authors: Tang, C. / Ndassa, Y. / Summers, M.F.
#1: Journal: Science / Year: 1996
Title: Structure of the Amino-Terminal Core Domain of the HIV-1 Capsid Protein.
Authors: Gitti, R.K. / Lee, B.M. / Walker, J. / Summers, M.F. / Yoo, S. / Sundquist, W.I.
History
DepositionMar 22, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2002Provider: repository / Type: Initial release
SupersessionMar 26, 2004ID: 1GDS, 1GDY, 1GDZ
Revision 1.1Feb 5, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Mar 12, 2014Group: Source and taxonomy
Revision 1.3May 15, 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: GAG POLYPROTEIN


Theoretical massNumber of molelcules
Total (without water)16,7161
Polymers16,7161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST TARGET FUNCTION
RepresentativeModel #1

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Components

#1: Protein GAG POLYPROTEIN


Mass: 16716.189 Da / Num. of mol.: 1 / Fragment: AMINO-TERMINAL CORE DOMAIN RESIDUES 132 - 282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (NEW YORK-5 ISOLATE)
Strain: PNL4-3 / Cell line: CLONE 12 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12493
Sequence detailsGENBANK PID G902799 FOR GAG POLYPROTEIN PRECURSOR

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HMQC-NOESY-HSQC
121HSQC HNCA
131HN(CO)CA
141HNCO
151HNHA HMQC-NOESY-HSQC
161HSQC-NOESY-HSQC
171HMQC-NOESY-HMQC
NMR detailsText: HSQC HNCA, HN(CO)CA, HNCO, HNHA HMQC-NOESY-HSQC, HSQC-NOESY-HSQC, HMQC-NOESY-HMQC

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Sample preparation

Sample conditionsIonic strength: 10 mM / pH: 5.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
DYANAGUNTERT,WUTHRICHrefinement
DYANAstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: TORSION ANGLE DYNAMICS FOLLOWED BY ENERGY MINIMIZATION. GUNTERT, P., MUMENTHALER, C. WUTHRICH, K. (1997). TORSION ANGLE DYNAMICS FOR NMR STRUCTURE CALCULATION WITH THE NEW PROGRAM DYANA. J. ...Details: TORSION ANGLE DYNAMICS FOLLOWED BY ENERGY MINIMIZATION. GUNTERT, P., MUMENTHALER, C. WUTHRICH, K. (1997). TORSION ANGLE DYNAMICS FOR NMR STRUCTURE CALCULATION WITH THE NEW PROGRAM DYANA. J. MOL. BIOL. 273, 283-298.
NMR ensembleConformer selection criteria: LOWEST TARGET FUNCTION / Conformers calculated total number: 100 / Conformers submitted total number: 20

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