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- PDB-1lb0: NMR Structure of HIV-1 gp41 659-671 13-mer peptide -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1lb0
TitleNMR Structure of HIV-1 gp41 659-671 13-mer peptide
ComponentsGP41
KeywordsVIRAL PROTEIN / 3-10 helix / gp41 envelope protein
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
MethodSOLUTION NMR / Distance geometry simulated annealing
AuthorsBiron, Z.
CitationJournal: Biochemistry / Year: 2002
Title: A Monomeric 3(10)-Helix Is Formed in Water by a 13-Residue Peptide Representing the Neutralizing Determinant of HIV-1 on gp41(,).
Authors: Biron, Z. / Khare, S. / Samson, A.O. / Hayek, Y. / Naider, F. / Anglister, J.
History
DepositionApr 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GP41


Theoretical massNumber of molelcules
Total (without water)1,6181
Polymers1,6181
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 / -
Representative

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Components

#1: Protein/peptide GP41 / / Transmembrane glycoprotein


Mass: 1617.820 Da / Num. of mol.: 1 / Fragment: Residues 659-671 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in HIV-1 virus.
References: UniProt: P31872

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
13.5mM gp41659-671; 50mM 50mM ammonium acetate buffer.95% H2O/5% D2O
25 mM gp41659-671; 50mM 50mM ammonium acetate buffer95% H2O/5% D2O
Sample conditionsIonic strength: 0.1mM / pH: 7.7 / Pressure: 1 atm / Temperature: 277 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 software
NameVersionDeveloperClassification
AURELIAamix 2.8.11Brukerdata analysis
XwinNMR3Brukerprocessing
CNS1.1A.T.Brungerstructure solution
CNSA.T.Brungerrefinement
RefinementMethod: Distance geometry simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 212 restraints, 202 are NOE-derived distance constraints, 9 dihedral angle restraints,1 distance restraint from hydrogen bonds.
NMR ensembleConformers submitted total number: 1

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