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- PDB-1im7: Solution structure of synthetic cyclic peptide mimicking the loop... -

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Basic information

Entry
Database: PDB / ID: 1im7
TitleSolution structure of synthetic cyclic peptide mimicking the loop of HIV-1 gp41 glycoprotein envelope
ComponentsGP41-PARENT PEPTIDE ACE-ILE-TRP-GLY-CYS-SER-GLY-LYS-LEU-ILE-CYS-THR-THR-ALA
KeywordsVIRAL PROTEIN / 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 ...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 energy minimisation
Model type detailsminimized average
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 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2002Provider: 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 1.4Nov 20, 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: GP41-PARENT PEPTIDE ACE-ILE-TRP-GLY-CYS-SER-GLY-LYS-LEU-ILE-CYS-THR-THR-ALA


Theoretical massNumber of molelcules
Total (without water)1,3801
Polymers1,3801
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 / 50target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide GP41-PARENT PEPTIDE ACE-ILE-TRP-GLY-CYS-SER-GLY-LYS-LEU-ILE-CYS-THR-THR-ALA


Mass: 1379.668 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS SEQUENCE OCCURS NATURALLY IN HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
References: UniProt: P12488
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques. NOESY experiments with mixing times from 80ms to 800ms were reccorded in order to define the best conditions avoiding spin diffusion.

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Sample preparation

DetailsContents: 2mM and 4mM peptide ; 500 ul DMSO-D6 / Solvent system: DMSO-D6
Sample conditionsPressure: ambient / Temperature: 298 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 AVANCEBrukerAVANCE4001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker brmHcollection
XwinNMR2.6Bruker brmHprocessing
XEASYBartels C.,Xia T. , Billeter M., Guentert P. and Wthrich K. J. Biomolecular 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 dynamics energy minimisation / Software ordinal: 1
Details: 50 initial random strucutres were produced using simulated annealing in DYANA software.Refinement was done with 500 steps restrained minimization , 35ps MD in vacuo at 300K for equilibration ...Details: 50 initial random strucutres were produced using simulated annealing in DYANA software.Refinement was done with 500 steps restrained minimization , 35ps MD in vacuo at 300K for equilibration and 200ps MD under NMR restraints and 750 steps conjugeted gradient EM using DISCOVER module of MSI software.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 1

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