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- PDB-1l6n: STRUCTURE OF THE N-TERMINAL 283-RESIDUE FRAGMENT OF THE HIV-1 GAG... -

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Basic information

Entry
Database: PDB / ID: 1l6n
TitleSTRUCTURE OF THE N-TERMINAL 283-RESIDUE FRAGMENT OF THE HIV-1 GAG POLYPROTEIN
ComponentsGag PolyproteinGroup-specific antigen
KeywordsVIRAL PROTEIN / gag / matrix / capsid / maturation
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / structural molecule activity / virion membrane / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Immunodeficiency lentiviruses, gag gene matrix protein p17 / 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) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain ...Immunodeficiency lentiviruses, gag gene matrix protein p17 / 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) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / DNA polymerase; domain 1 / 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 1
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsTang, C. / Ndassa, Y. / Summers, M.F.
CitationJournal: 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.
History
DepositionMar 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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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)32,3931
Polymers32,3931
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Gag Polyprotein / Group-specific antigen


Mass: 32392.873 Da / Num. of mol.: 1 / Fragment: Residues 1-283
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: gag / Plasmid: p11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q72497

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2114D 13C-separated NOESY
1214D 13C/15N-separated NOESY
1343D 15N-separated NOESY
1434D 15N/15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM U-15N,13C gag283, 50mM acetate buffer(pH5.0), 100mM NaCl, 5mM BME95% H2O/5% D2O
21mM U-15N,13C gag283, 50mM acetate buffer(pH5.0), 100mM NaCl, 5mM BME100% D2O
31mM U-15N,2H gag283, 50mM acetate buffer(pH5.0), 100mM NaCl, 5mM BME95% H2O/5% D2O
41mM U-15N gag283, 50mM acetate buffer(pH5.0), 100mM NaCl, 5mM BME95% H2O/5% D2O
Sample conditionsIonic strength: 50 / pH: 5.0 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
NMRPipe2Delaglioprocessing
XwinNMR2.6collection
DYANA1.5Guentert,P., Mumenthaler,C., & Wuthrich,K.refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: 20 CONFORMERS COMPATIBLE WITH THE NMR CONSTRAINTS WERE CALCULATED USING DYANA 1.5 AND THE STANDARD TORSION ANGLE SIMULATED ANNEALING PROTOCOL. PRELIMINARY CALCULATIONS WERE CARRIED OUT ...Details: 20 CONFORMERS COMPATIBLE WITH THE NMR CONSTRAINTS WERE CALCULATED USING DYANA 1.5 AND THE STANDARD TORSION ANGLE SIMULATED ANNEALING PROTOCOL. PRELIMINARY CALCULATIONS WERE CARRIED OUT INDEPENDENTLY FOR MATRIX AND CAPSID N-TERMINAL DOMAINS OF THE PROTEIN. INITIALLY ONLY NOE DISTANCE CONSTRAINTS WERE IMPOSED. UNAMBIGUOUS H-BONDS WERE ALSO INCORPORATED TO REINFORCE CANONICAL SECONDARY STRUCTURE. THE INITIAL STRUCTURES WERE THEN USED TO ASSESS THE ACCURACY OF THE TORSION ANGLE CONSTRAINTS GENERATED BY ANALYSIS OF HA, CA, CB, CO AND N CHEMICAL SHIFTS WITH THE PROGRAM TALOS. FINALLY, ALL THE CONSTRAINTS WERE USED TO CALCULATE THE STRUCTURE OF THE WHOLE PROTEIN.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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