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- PDB-1meq: HIV gp120 C5 -

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Basic information

Entry
Database: PDB / ID: 1meq
TitleHIV gp120 C5
ComponentsExterior Membrane Glycoprotein (GP120)
KeywordsVIRAL PROTEIN / HIV / AIDS / gp120 / gp41
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / torsion angle dynamics
Model type detailsminimized average
AuthorsCaffrey, M. / Jacobs, A. / Guilhaudis, L.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Solution Structure of the HIV gp120 C5 Domain
Authors: Guilhaudis, L. / Jacobs, A. / Caffrey, M.
History
DepositionAug 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 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: 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)2,6671
Polymers2,6671
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)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Exterior Membrane Glycoprotein (GP120)


Mass: 2667.245 Da / Num. of mol.: 1 / Fragment: Residues (484-506) / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Human immunodeficiency virus type 1 (HIV-1).
References: UniProt: P19549

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: 1mM HIV gp120 C5 at natural abundance
Solvent system: 40% TFE, 50 mM phoshpate buffer, 55% H2O, 5% D2O
Sample conditionsIonic strength: 70 mM / pH: 6 / Pressure: 1 atm / Temperature: 300 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
CNS1Brungerstructure solution
CNSBrunger, A., Adams, P., Clore, G., DeLano, W., Gros, P., Grosse-Kunstleve, R., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N., Read, R., Rice, L., Simonson, T. & Warren, G.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: 190 distance restraints, 47 dihedral restraints
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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