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- PDB-1j8n: Solution structure of beta3-analogue peptide corresponding to the... -

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Basic information

Entry
Database: PDB / ID: 1j8n
TitleSolution structure of beta3-analogue peptide corresponding to the gp41 600-612 loop of HIV.
ComponentsHIV1 GP41 HSER analogue peptide Ace-Ile-Trp-Gly-Cys-beta3Ser-Gly-Lys-Leu-Ile-Cys-Thr-Thr-Ala
KeywordsVIRAL PROTEIN / beta peptide / gp41 / cyclic peptide
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
DepositionMay 22, 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 5, 2011Group: Other
Revision 1.4Jun 24, 2020Group: Data collection / Database references / Derived calculations
Category: pdbx_nmr_software / pdbx_nmr_spectrometer ...pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV1 GP41 HSER analogue peptide Ace-Ile-Trp-Gly-Cys-beta3Ser-Gly-Lys-Leu-Ile-Cys-Thr-Thr-Ala


Theoretical massNumber of molelcules
Total (without water)1,3941
Polymers1,3941
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)27 / 50target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide HIV1 GP41 HSER analogue peptide Ace-Ile-Trp-Gly-Cys-beta3Ser-Gly-Lys-Leu-Ile-Cys-Thr-Thr-Ala


Mass: 1393.694 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PARENT SEQUENCE IWGCSGKLICTTA OCCURS IN HIV GP41 PROTEIN. This analogue contains a modified residue BSE which is a beta3-Ser (i.e. with an additional CH2 between NH and Calpha).
References: UniProt: P12488

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
122DQF-COSY
1322D NOESY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES. NOESY EXPERIMENTS WITH MIXING TIMES FROM 80MS TO 800MS WERE RECORDED IN ORDER TO DEFINE THE BEST CONDITIONS IN ORDER TO AVOID SPIN DIFFUSION.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM peptide ; 500ul DMSO-D6DMSO-D6
24mM peptide ; 500ul DMSO-D6DMSO-D6
Sample conditionsPressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
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
XEASY1.2Bartels C., Xia T., Billeter M., Guentert P. and Wuethrich K., (1995)J. Biomolecular NMR 5, 1-10data analysis
DYANA1.5Guentert P., Mumenthaler C., Wuethrich K.refinement
Discover3Molecular Simulation Inc., San Diegorefinement
RefinementMethod: torsion angle dynamics, molecular dynamics, energy minimization
Software ordinal: 1
Details: 50 INITIAL RANDOM STRUCTURES WERE CALCULATED USING SIMULATED ANNEALING IN DYANA SOFTWARE. REFINEMENT WAS DONE WITH 500 STEPS RESTRAINED MINIMIZATION, 35PS MD IN VACUO AT 300K FOR ...Details: 50 INITIAL RANDOM STRUCTURES WERE CALCULATED USING SIMULATED ANNEALING IN DYANA SOFTWARE. REFINEMENT WAS DONE WITH 500 STEPS RESTRAINED MINIMIZATION, 35PS MD IN VACUO AT 300K FOR EQUILIBRATION, 200PS MD UNDER NMR RESTRAINTS, AND 750PS CONJUGATED GRADIENT EM USING DISCOVER MODULE OF MSI SOFTWARE.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 27

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