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- PDB-1jau: NMR Solution Structure of the Trp-Rich Peptide of HIV gp41 Bound ... -

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Basic information

Entry
Database: PDB / ID: 1jau
TitleNMR Solution Structure of the Trp-Rich Peptide of HIV gp41 Bound to DPC Micelles
ComponentsTRANSMEMBRANE GLYCOPROTEIN (GP41)
KeywordsVIRAL PROTEIN / amphipathic alpha helix
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 / distance geometry, simulated annealing, molecular dynamics, matrix relaxation
AuthorsSchibli, D.J. / Montelaro, R.C. / Vogel, H.J.
CitationJournal: Biochemistry / Year: 2001
Title: The membrane-proximal tryptophan-rich region of the HIV glycoprotein, gp41, forms a well-defined helix in dodecylphosphocholine micelles.
Authors: Schibli, D.J. / Montelaro, R.C. / Vogel, H.J.
History
DepositionMay 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSMEMBRANE GLYCOPROTEIN (GP41)


Theoretical massNumber of molelcules
Total (without water)2,5701
Polymers2,5701
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)40 / 200structures with the lowest energy
Representative

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Components

#1: Protein/peptide TRANSMEMBRANE GLYCOPROTEIN (GP41)


Mass: 2569.979 Da / Num. of mol.: 1 / Fragment: residues 665-683 / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence of the peptide is naturally found in Human Immunodeficiency Virus (HIV).
References: UniProt: P04624
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1422D NOESY
1522D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.6 mM synthetic gp41 peptide, 200 mM perdeuterated dodecylphosphocholine90% H2O/10% D2O
21.6 mM synthetic gp41 peptide, 200 mM perdeuterated dodecylphosphocholine100% D2O
Sample conditionsIonic strength: 200 mM DPC-d38 / pH: 3.51 / Pressure: ambient / Temperature: 310 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 AVANCEBrukerAVANCE5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe1.8F.Delaglio, S.Grzesiek, G.Vuister, G.Zhu, J.Pfeifer, A.Baxprocessing
NMRView4.1.3B.Johnson, R.A.Blevinsdata analysis
CNS1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenstructure solution
ARIA1M.Nilges, J.Linge, S.O'Donoghueiterative matrix relaxation
CNS1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, matrix relaxation
Software ordinal: 1
Details: Structures were initially generated using CNS. Ambiguous and unassigned noe constraints were then used in conjuction with matrix relaxation analysis using the program ARIA.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 40

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