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- PDB-6ftk: Gp36-MPER -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6ftk
TitleGp36-MPER
ComponentsEnvelope proteinViral envelope
KeywordsVIRAL PROTEIN / MPER / Gp36 / FIV
Function / homology
Function and homology information


viral process / membrane => GO:0016020 / viral envelope / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
Envelope glycoprotein, lentivirus / Lentivirus surface glycoprotein / Retroviral envelope protein GP41-like
Similarity search - Domain/homology
Biological speciesFeline immunodeficiency virus
MethodSOLUTION NMR / torsion angle dynamics / simulated annealing
AuthorsD'Ursi, A.M. / Grimaldi, M.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Commission261863 Netherlands
CitationJournal: Int J Mol Sci / Year: 2020
Title: NMR Structure of the FIV gp36 C-Terminal Heptad Repeat and Membrane-Proximal External Region.
Authors: Grimaldi, M. / Buonocore, M. / Scrima, M. / Stillitano, I. / D'Errico, G. / Santoro, A. / Amodio, G. / Eletto, D. / Gloria, A. / Russo, T. / Moltedo, O. / Remondelli, P. / Tosco, A. / Wienk, ...Authors: Grimaldi, M. / Buonocore, M. / Scrima, M. / Stillitano, I. / D'Errico, G. / Santoro, A. / Amodio, G. / Eletto, D. / Gloria, A. / Russo, T. / Moltedo, O. / Remondelli, P. / Tosco, A. / Wienk, H.L.J. / D'Ursi, A.M.
History
DepositionFeb 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Apr 1, 2020Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_spectrometer.model
Revision 1.3Jul 29, 2020Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope protein


Theoretical massNumber of molelcules
Total (without water)6,1261
Polymers6,1261
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5600 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)6 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Envelope protein / Viral envelope


Mass: 6126.001 Da / Num. of mol.: 1 / Mutation: M737L, M751L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline immunodeficiency virus / Gene: env / Plasmid: pET-31b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: D0E8G2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic13D NOESY
131isotropic13D NOESY 13C-HSQC
141isotropic1NOESY 15N-HSQC
151isotropic23D CBCA(CO)NH
181isotropic23D HN(CA)CB
171isotropic23D HNCO
161isotropic23D HN(CA)CO
1101isotropic23D HBHA(CO)NH
191isotropic23D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 2 g/L [U-95% 13C] glucose, 1 g/L [U-98% 15N] ammonium sulfate, 90% H2O/10% D2O
Details: 90% DPC-d38/ 10% SDS-d25 (27mM/3mM) micelle solution
Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 g/Lglucose[U-95% 13C]1
1 g/Lammonium sulfate[U-98% 15N]1
Sample conditionsIonic strength: 0.15 Not defined / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III9001TCI cryoprobe
Bruker AVANCE IIIBrukerAVANCE III6002TXI probe

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3Goddardchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
TALOS+Cornilescu, Delaglio and Baxrefinement
Refinement
MethodSoftware ordinal
torsion angle dynamics3
simulated annealing2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 6

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