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- PDB-5nwu: NMR assignment and structure of a peptide derived from the fusion... -

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Basic information

Entry
Database: PDB / ID: 5nwu
TitleNMR assignment and structure of a peptide derived from the fusion peptide of HIV-1 gp41 in the presence of hexafluoroisopropanol
ComponentswtFP-tag,Gp41
KeywordsVIRAL PROTEIN / Envelope glycoprotein gp41 / fusion peptide / STRUCTURE FROM CYANA 2.1
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / 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 / Gp41
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing
AuthorsJimenez, M.A. / Serrano, S. / Nieva, J.L. / Huarte, N.
Funding support Spain, 1items
OrganizationGrant numberCountry
MINECOCTQ2014-52633P Spain
CitationJournal: Biochemistry / Year: 2017
Title: Structure-Related Roles for the Conservation of the HIV-1 Fusion Peptide Sequence Revealed by Nuclear Magnetic Resonance.
Authors: Serrano, S. / Huarte, N. / Rujas, E. / Andreu, D. / Nieva, J.L. / Jimenez, M.A.
History
DepositionMay 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Oct 30, 2019Group: Data collection / Database references / Category: pdbx_database_related / pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 1.4Dec 18, 2019Group: Source and taxonomy / Category: pdbx_entity_src_syn
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: wtFP-tag,Gp41


Theoretical massNumber of molelcules
Total (without water)3,8221
Polymers3,8221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area280 Å2
ΔGint4 kcal/mol
Surface area3890 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide wtFP-tag,Gp41


Mass: 3822.411 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Residues 1-15 are derived from gp41 fusion peptide and correspond to residues 514-528 of gp41. Residues 19-35 are derived from gp41 MPER region and correspond to residues 655-671 of gp41. ...Details: Residues 1-15 are derived from gp41 fusion peptide and correspond to residues 514-528 of gp41. Residues 19-35 are derived from gp41 MPER region and correspond to residues 655-671 of gp41. Residues 16-18 are the linker sequence.
Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q69894, UniProt: P04578*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H COSY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-13C HSQC aliphatic
151isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 0.6 mM wtFP-tag, 25 % [U-98% 2H] HFIP, 2.0 mM HEPES, 67.5 % H2O, 7.5 % [U-99% 2H] D2O, 0.1 mM DSS, hexafluoroisopropanol/water
Details: 25 % hexafluoroisopropanol / Label: wtFP-tag / Solvent system: hexafluoroisopropanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMwtFP-tagnatural abundance1
25 %HFIP[U-98% 2H]1
2.0 mMHEPESnatural abundance1
67.5 %H2Onatural abundance1
7.5 %D2O[U-99% 2H]1
0.1 mMDSSnatural abundance1
Sample conditionsIonic strength: 2 mM / Label: conditions_1 / pH: 6.8 pH* / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz / Details: equipped with a cryoprobe

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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