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- PDB-1jcp: Solution structure of the lactam analogue EDap of HIV gp41 600-61... -

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Basic information

Entry
Database: PDB / ID: 1jcp
TitleSolution structure of the lactam analogue EDap of HIV gp41 600-612 loop.
ComponentsEdap : ACE-Ile-Trp-Glu-Ser-Gly-Lys-Leu-Ile-Dap-Thr-Thr-Ala ANALOGUE OF HIV GP41
KeywordsVIRAL PROTEIN / cyclic peptide / gp41 / HIV / lactam bond / pseudopeptide.
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, molecular dynamics, energy minimization.
AuthorsPhan Chan Du, A. / Limal, D. / Semetey, V. / Dali, H. / Jolivet, M. / Desgranges, C. / Cung, M.T. / Briand, J.P. / Petit, M.C. / Muller, S.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structural and immunological characterisation of heteroclitic peptide analogues corresponding to the 600-612 region of the HIV envelope gp41 glycoprotein.
Authors: Du, A.P. / Limal, D. / Semetey, V. / Dali, H. / Jolivet, M. / Desgranges, C. / Cung, M.T. / Briand, J.P. / Petit, M.C. / Muller, S.
History
DepositionJun 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Edap : ACE-Ile-Trp-Glu-Ser-Gly-Lys-Leu-Ile-Dap-Thr-Thr-Ala ANALOGUE OF HIV GP41


Theoretical massNumber of molelcules
Total (without water)1,3891
Polymers1,3891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Edap : ACE-Ile-Trp-Glu-Ser-Gly-Lys-Leu-Ile-Dap-Thr-Thr-Ala ANALOGUE OF HIV GP41


Mass: 1388.589 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The parent peptide (IWGCSGKLICTTA) occurs naturally in HIV gp41.
References: UniProt: P12488

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D NOESY
131TOCSY
NMR detailsText: Classical 2D homonuclear NMR techniques were used. Different NOESY experiments with different mixing times from 80ms to 800ms were recorded in order to determine the best conditions without spin diffusion.

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Sample preparation

DetailsContents: 4mM peptide in 500ul solvent / Solvent system: 100% DMSO-D6
Sample conditionsPressure: atmospheric atm / Temperature: 298 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 AVANCEBrukerAVANCE4001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker GMBHcollection
XwinNMR2.6Bruker GMBHprocessing
XEASY1.2Bartels C., Billeter M., Guentert P. and Wuethrich K. (1995) J. Biomol. NMR, 5, 1-10data analysis
DYANA1.5Guentert, Mumenthaler C. and Wuethrich K. (1997) J.Mol. Biol. 273, 283-298refinement
Discover3MSI, San Diegorefinement
RefinementMethod: torsion angle dynamics, molecular dynamics, energy minimization.
Software ordinal: 1
Details: 50 initial structures were generated using DYANA software, followed by 500 ps restrained energy minimization. Then using DISCOVER 35 ps MD, 750ps conjugated gradient EM .
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20

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