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- PDB-2esx: The structure of the V3 region within gp120 of JR-FL HIV-1 strain... -

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Basic information

Entry
Database: PDB / ID: 2esx
TitleThe structure of the V3 region within gp120 of JR-FL HIV-1 strain (minimized average structure)
ComponentsEnvelope polyprotein GP160
KeywordsVIRAL PROTEIN / HIV-1 / JR-FL / V3 / 447-52D / antibody
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / positive regulation of cell growth / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / positive regulation of cell growth / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / distance geometry simulated annealing
Model type detailsminimized average
AuthorsRosen, O. / Sharon, M. / Samson, A.O. / Quadt, S.R. / Anglister, J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Molecular switch for alternative conformations of the HIV-1 V3 region: Implications for phenotype conversion.
Authors: Rosen, O. / Sharon, M. / Quadt-Akabayov, S.R. / Anglister, J.
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope polyprotein GP160


Theoretical massNumber of molelcules
Total (without water)2,1081
Polymers2,1081
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)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Envelope polyprotein GP160


Mass: 2108.401 Da / Num. of mol.: 1 / Fragment: V3 of GP120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: JR-FL / Gene: ENV / Plasmid: pM4-V3JRFL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS / References: UniProt: P20871, UniProt: O36236*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
1432D-NOESY AROMATIC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4mM V3JR-FL-447-52D complex U-15N5% D2O, 95% H2O
20.4mM V3JR-FL-447-52D complex U-15N-13C5% D2O, 95% H2O
30.4mM V3JR-FL-447-52D complex U-15N-13C100% D2O
Sample conditionsIonic strength: 10mM acetic acid / pH: 5 / Temperature: 305 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brungerstructure solution
XwinNMR3Brukercollection
NMRView5.2.2Johnsondata analysis
CNS1.1Brungerrefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: The strcuture is based on 305 restraints, 25 dihedral angles and 2 hydrogen bond
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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