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- PDB-1p5a: Conformational Mapping of the N-terminal Peptide of HIV-1 GP41 in... -

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Entry
Database: PDB / ID: 1p5a
TitleConformational Mapping of the N-terminal Peptide of HIV-1 GP41 in lipid detergent and aqueous environments using 13C-enhanced Fourier Transform Infrared Spectroscopy
ComponentsEnvelope polyprotein GP160
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 / 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
MethodINFRARED SPECTROSCOPY / molecular dynamics
AuthorsGordon, L.M. / Mobley, P.W. / Lee, W. / Eskandari, S. / Kaznessis, Y.N. / Sherman, M.A. / Waring, A.J.
Citation
Journal: Protein Sci. / Year: 2004
Title: Conformational mapping of the N-terminal peptide of HIV-1 gp41 in lipid detergent and aqueous environments using 13C-enhanced Fourier transform infrared spectroscopy.
Authors: Gordon, L.M. / Mobley, P.W. / Lee, W. / Eskandari, S. / Kaznessis, Y.N. / Sherman, M.A. / Waring, A.J.
#1: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 2002
Title: CONFORMATIONAL MAPPING OF THE N-TERMINAL PEPTIDE OF HIV-1 GP41 IN MEMBRANE ENVIRONMENTS USING 13C-ENHANCED FOURIER TRANSFORM INFRARED SPECTROSCOPY
Authors: GORDON, L.M. / MOBLEY, P.W. / PILPA, R. / SHERMAN, M.A. / WARING, A.J.
History
DepositionApr 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 250REMARK: THIS STRUCTURE WAS DETERMINED BY MEANS OF 13C-ENHANCED FOURIER TRANSFORM INFRARED ...REMARK: THIS STRUCTURE WAS DETERMINED BY MEANS OF 13C-ENHANCED FOURIER TRANSFORM INFRARED SPECTROSCOPY (FTIR). DATA SET CONSISTS OF 19 CONFORMERS DERIVED FROM MOLECULAR DYNAMICS IN A MODELED SDS MICELLE SURROUNDED BY WATER WITH PEPTIDE BACKBONE CONSTRAINTS FROM FTIR. EXPERIMENTAL DETAILS EXPERIMENT TYPE : INFRARED SPECTROSCOPY TEMPERATURE (KELVIN) : 298 PH : 7.4 IONIC STRENGTH : 0.271 PRESSURE : AMBIENT SAMPLE 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. EXPERIMENTS CONDUCTED : 13C-ISOTOPE ENHANCED FTIR SPECTROMETER FIELD STRENGTH : NULL SPECTROMETER MODEL : RESEARCH SERIES SPECTROMETER MANUFACTURER : MATTSON FTIR STRUCTURE DETERMINATION. SOFTWARE USED : WINFIRST FTIR CURVE FITTING SOFTWARE METHOD USED : MOLECULAR DYNAMICS CONFORMERS, NUMBER CALCULATED : 20 CONFORMERS, NUMBER SUBMITTED : 19 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK: THE COORDINATES IN THIS ENTRY WERE GENERATED FROM 13-C INDUCED SPECTRAL SHIFTS WHICH GIVE RESIDUE-SPECIFIC SECONDARY STRUCTURE INFORMATION. PEPTIDE CONCENTRATION WAS 47 MICROMOLAR. PEPTIDE/SDS RATIO WAS 1/200. FTIR SPECTRA WERE AVERAGED OVER 256 SCANS AT A GAIN OF 4 AND A RESOLUTION OF 2 CM-1

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope polyprotein GP160


Theoretical massNumber of molelcules
Total (without water)2,1231
Polymers2,1231
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 20structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Envelope polyprotein GP160 / N-terminal fusion peptide of HIV-1 GP41


Mass: 2123.481 Da / Num. of mol.: 1 / Fragment: residues 519-541 / Source method: obtained synthetically
Details: The sequence of this peptide occurs naturally in human immunodeficiency virus glycoprotein 41.
References: UniProt: P03377

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Experimental details

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Experiment

ExperimentMethod: INFRARED SPECTROSCOPY
NMR experimentType: 13C-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. Peptide concentration was 47 micromolar. Peptide/SDS ...Text: The coordinates in this entry were generated from 13-C induced spectral shifts which give residue-specific secondary structure information. Peptide concentration was 47 micromolar. Peptide/SDS ratio was 1/200. FTIR spectra were averaged over 256 scans at a gain of 4 and a resolution of 2 cm-1

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Sample preparation

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: 94 mM SDS (sodium dodecyl sulfate) in deuterated PBS (phosphate buffered saline), where PBS is 120 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4
Sample conditionsIonic strength: 0.271 / pH: 7.4 / Pressure: ambient / Temperature: 298
Crystal grow
*PLUS
Method: spectroscopy / Details: spectroscopy

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Mattson FTIR Research Series / Manufacturer: Mattson FTIR / Model: Research Series

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Processing

NMR software
NameVersionDeveloperClassification
WinfirstFTIR curve fitting softwareKauppine et al.data analysis
CHARMMc28b2Brooks et al.refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: The system of more than 16,000 atoms (peptide, SDS micelle, water, sodium counterions) was simulated for 2.5 nanoseconds at a constant pressure P=1 atm and constant temperature T=303.15 K.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 20 / Conformers submitted total number: 19

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