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

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Basic information

Entry
Database: PDB / ID: 5nww
TitleNMR assignment and structure of a peptide derived from the fusion peptide of HIV-1 gp41 in the presence of dodecylphosphocholine micelles
ComponentsscrFP-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 / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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 / 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 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 16, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: scrFP-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 area320 Å2
ΔGint5 kcal/mol
Surface area3670 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 scrFP-tag,Gp41


Mass: 3822.411 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Residues 1-4 and 12-15 are derived from gp41 fusion peptide and correspond to residues 514-517 and 525-528 of gp41. Residues 5-11 are residues 518-524 of gp41 in a scrambled order. Residues ...Details: Residues 1-4 and 12-15 are derived from gp41 fusion peptide and correspond to residues 514-517 and 525-528 of gp41. Residues 5-11 are residues 518-524 of gp41 in a scrambled order. 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
Has protein modificationY

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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

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Sample preparation

DetailsType: micelle
Contents: 0.6 mM scrFP-tag, 20 mM [U-98% 2H] DPC, 2.0 mM HEPES, 90 % H2O, 10 % [U-99% 2H] D2O, 0.1 mM DSS, 90% H2O/10% D2O
Details: DPC micelles / Label: scrFP-tag / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMscrFP-tagnatural abundance1
20 mMDPC[U-98% 2H]1
2.0 mMHEPESnatural abundance1
90 %H2Onatural abundance1
10 %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 Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
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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