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- PDB-1j9v: Solution structure of a lactam analogue (DabD) of HIV gp41 600-61... -

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Basic information

Entry
Database: PDB / ID: 1j9v
TitleSolution structure of a lactam analogue (DabD) of HIV gp41 600-612 loop.
ComponentsDabD (Ace)IWG(DAB)SGKLIDTTA ANALOGUE OF HIV GP41
KeywordsVIRAL PROTEIN / lactam peptide / lactam bond / HIV / gp41 / cyclic peptide
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 / Torsion angle dinamics, 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 29, 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: 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_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DabD (Ace)IWG(DAB)SGKLIDTTA ANALOGUE OF HIV GP41


Theoretical massNumber of molelcules
Total (without water)1,3891
Polymers1,3891
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)49 / 50target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide DabD (Ace)IWG(DAB)SGKLIDTTA ANALOGUE OF HIV GP41


Mass: 1388.589 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The parent peptide (IWGCSGKLICTTA) occurs in HIV gp41 glycoprotein.
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
232TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques. Different NOESY experiments with mixing times from 80 ms to 800 ms were recorded, in order to determined the best ...Text: This structure was determined using standard 2D homonuclear techniques. Different NOESY experiments with mixing times from 80 ms to 800 ms were recorded, in order to determined the best conditions avoiding spin diffusion.

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Sample preparation

DetailsContents: 3,5 mM peptide in 500ul DMSO-D6 / Solvent system: DMSO-D6
Sample conditionsPressure: ambient / 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., Xia T., Billeter M., Guentert P. and Wuethrich K. (1995) J. Biomol. NMR, 5, 1-10data analysis
DYANA1.5Guentert P., Mumenthaler C. and Wuethrich K. (1997) J. Mol. Biol. 273, 283-298refinement
Discover3Molecular Simulation Inc. San Diegorefinement
RefinementMethod: Torsion angle dinamics, molecular dynamics, energy minimization.
Software ordinal: 1
Details: 50 INITIAL RANDOM STRUCTURES WERE GENERATED USING SIMULATED ANNEALING IN DYANA SOFTWARE, FOLLOWED BY 500PS RESTRAINED MINIMIZATION, 35PS MD IN VACUO AT 300K, 200 PS MD UNDER NMR RESTRAINTS ...Details: 50 INITIAL RANDOM STRUCTURES WERE GENERATED USING SIMULATED ANNEALING IN DYANA SOFTWARE, FOLLOWED BY 500PS RESTRAINED MINIMIZATION, 35PS MD IN VACUO AT 300K, 200 PS MD UNDER NMR RESTRAINTS AND 750 STEPS CONJUGATED GRADIENT EM USING DISCOVER OF MSI SOFTWARE
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 49

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