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- PDB-1erf: CONFORMATIONAL MAPPING OF THE N-TERMINAL FUSION PEPTIDE OF HIV-1 ... -

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Basic information

Entry
Database: PDB / ID: 1erf
TitleCONFORMATIONAL MAPPING OF THE N-TERMINAL FUSION PEPTIDE OF HIV-1 GP41 USING 13C-ENHANCED FOURIER TRANSFORM INFRARED SPECTROSCOPY (FTIR)
ComponentsTRANSMEMBRANE GLYCOPROTEIN
KeywordsVIRAL PROTEIN / human immunodeficiency virus (HIV-1) / viral fusion peptide / gp41
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
MethodINFRARED SPECTROSCOPY / molecular dynamics, simulated annealing
AuthorsGordon, L.M. / Mobley, P.W. / Pilpa, R. / Sherman, M.A. / Waring, A.J.
CitationJournal: Biochim.Biophys.Acta / Year: 2002
Title: Conformational mapping of the N-terminal peptide of HIV-1 gp41 in membrane environments using (13)C-enhanced Fourier transform infrared spectroscopy.
Authors: Gordon, L.M. / Mobley, P.W. / Pilpa, R. / Sherman, M.A. / Waring, A.J.
History
DepositionApr 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: TRANSMEMBRANE GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)2,1231
Polymers2,1231
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)17 / 31structures with acceptable covalent geometry
RepresentativeModel #9closest to the average

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Components

#1: Protein/peptide TRANSMEMBRANE GLYCOPROTEIN / GP41


Mass: 2123.481 Da / Num. of mol.: 1 / Fragment: N-TERMINAL FUSION PEPTIDE (RESIDUES 519-541) / Mutation: C-TERMINUS HAS BEEN AMIDATED / Source method: obtained synthetically
Details: The sequence of this peptide occurs naturally in human immunodeficiency virus glycoprotein 41.
References: UniProt: P03377
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: INFRARED SPECTROSCOPY
NMR experimentType: 13-C isotope enhanced FTIR
NMR detailsText: The coordinates in this entry were generated from 13-C induced spectral shifts which give residue-specific secondary structure information.

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Sample preparation

CrystalDescription: This structure was determined by means of 13C-enhanced Fourier Transform Infrared Spectroscopy (FTIR). Data set consists of 17 conformers derived from simulated annealing with constraints from FTIR.
DetailsContents: THIS STRUCTURE WAS DETERMINED USING 13-C ISOTOPE ENHANCED FTIR SPECTROSCOPY ON A FAMILY OF SELECTIVELY LABELED CHEMICALLY SYNTHESIZED PEPTIDES. 13-C CARBONYL LABELS INCLUDED RESIDUES ...Contents: THIS STRUCTURE WAS DETERMINED USING 13-C ISOTOPE ENHANCED FTIR SPECTROSCOPY ON A FAMILY OF SELECTIVELY LABELED CHEMICALLY SYNTHESIZED PEPTIDES. 13-C CARBONYL LABELS INCLUDED RESIDUES 519,521,523,524,525,526,527,528,529,530,531,532,533,534,538,539.
Solvent system: 70% hexafluoroisopropanol (HFIP), 29.9% water, 0.1% formic acid (v/v)
Sample conditionsIonic strength: 0 / pH: 7 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: infrared spectroscopy

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Data collection

NMR spectrometerType: Mattson FTIR Research Series / Manufacturer: Mattson FTIR / Model: Research Series / Field strength: 0 MHz

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Processing

NMR software
NameVersionDeveloperClassification
WinfirstFTIR curve fitting softwareKauppine et al.data analysis
Discover2.9.7Molecular Simulations, Inc. (San Diego, CA)refinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
Details: Molecular dynamics (simulated annealing) was used to generate an ensemble of conformers consistent with the FTIR data.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 31 / Conformers submitted total number: 17

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