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- PDB-1u6u: NMR structure of a V3 (IIIB isolate) peptide bound to 447-52D, a ... -

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Basic information

Entry
Database: PDB / ID: 1u6u
TitleNMR structure of a V3 (IIIB isolate) peptide bound to 447-52D, a human HIV-1 neutralizing antibody
ComponentsV3 peptide
KeywordsVIRAL PROTEIN / Beta hairpin
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 / 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 ...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 / 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 gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / distance geometry, simulated annealing
Model type detailsminimized average
AuthorsRosen, O. / Chill, J. / Sharon, M. / Kessler, N. / Mester, B. / Zolla-Pazner, S. / Anglister, J.
CitationJournal: Biochemistry / Year: 2005
Title: Induced fit in HIV-neutralizing antibody complexes: evidence for alternative conformations of the gp120 V3 loop and the molecular basis for broad neutralization.
Authors: Rosen, O. / Chill, J. / Sharon, M. / Kessler, N. / Mester, B. / Zolla-Pazner, S. / Anglister, J.
History
DepositionAug 2, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 5, 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_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: V3 peptide


Theoretical massNumber of molelcules
Total (without water)1,8601
Polymers1,8601
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 / -
Representativeminimized average structure

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Components

#1: Protein/peptide V3 peptide


Mass: 1860.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: IIIB isolate / Plasmid: pM4-V3IIIB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS / References: UniProt: P03377*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
10.5mM V3IIIB-447-52D complex, U-15N; PH 5, 10mM d-acetic acid, 0.02% NaN3; 5% D2O, 95% H2O5% D2O, 95% H20
20.5mM V3IIIB-447-52D complex, U-15N-13C; PH 5, 10mM d-acetic acid, 0.02% NaN3; 5% D2O, 95% H2O5% D2O, 95% H20
30.4mM V3IIIB-447-52D complex, U-15N-13C; PH 5, 10mM d-acetic acid, 0.02% NaN3; 100% D2O100% D2O
Sample conditionsIonic strength: 10mM acetic acid / pH: 5 / Pressure: ambient / 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
NMRPipe2.1Delagliodata analysis
CNS1.1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structure is based on 370 restraints, 21 dihedral angles and 5 hydrogen bonds
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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