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- PDB-1nj0: NMR structure of a V3 (MN isolate) peptide bound to 447-52D, a hu... -

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Basic information

Entry
Database: PDB / ID: 1nj0
TitleNMR structure of a V3 (MN isolate) peptide bound to 447-52D, a human HIV-1 neutralizing antibody
ComponentsExterior membrane glycoprotein(GP120)
KeywordsVIRAL PROTEIN / Peptide-Antibody complex / b-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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / 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
AuthorsSharon, M. / Kessler, N. / Levy, R. / Zolla-Pazner, S. / Gorlach, M. / Anglister, J.
CitationJournal: Structure / Year: 2003
Title: Alternative Conformations of HIV-1 V3 Loops Mimic beta Hairpins in Chemokines, Suggesting a Mechanism for Coreceptor Selectivity.
Authors: Sharon, M. / Kessler, N. / Levy, R. / Zolla-Pazner, S. / Gorlach, M. / Anglister, J.
History
DepositionDec 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exterior membrane glycoprotein(GP120)


Theoretical massNumber of molelcules
Total (without water)1,9071
Polymers1,9071
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)29 / 200structures with the lowest energy
Representative

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Components

#1: Protein/peptide Exterior membrane glycoprotein(GP120)


Mass: 1907.270 Da / Num. of mol.: 1 / Fragment: V3 loop (residues 309-324)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: ENV / Plasmid: pet11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P05877

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
3333D 13C-separated NOESY
242TROSY-HN(CA)CB & HBHA(CO)NH
252CT-CBCA(CO)NH
363(H)CCH-TOCSY & (H)CCH-COSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy, in which the peptide was labeled while the antibody remained unlabeled.

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N; 10mM sodium acetate buffer pH=595% H2O/5% D2O
2U-15N,13C; 10mM sodium acetate buffer pH=595% H2O/5% D2O
3U-15N,13C; 10mM sodium acetate buffer pH=599% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110mM 5ambient 308 K
210mM 5ambient 308 K
310mM 5ambient 308 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX5002

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Processing

NMR softwareName: CNS / Version: 1.1 / Developer: Brunger / Classification: refinement
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 29

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