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- PDB-5vwl: Solution NMR Structure of the Membrane Associated Segment of HIV-... -

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Basic information

Entry
Database: PDB / ID: 5vwl
TitleSolution NMR Structure of the Membrane Associated Segment of HIV-1 gp41 Cytoplasmic Tail
ComponentsCytoplasmic tail of HIV-1 gp41 protein
KeywordsVIRAL PROTEIN / alpha-helix / cytoplasmic tail / HIV-1 / envelope / plasma membrane
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane ...virus-mediated perturbation of host defense response => GO:0019049 / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 / plasma 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
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing
AuthorsSaad, J.S. / Murphy, R.E. / Samal, A. / Vlach, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM117837 United States
CitationJournal: Structure / Year: 2017
Title: Solution Structure and Membrane Interaction of the Cytoplasmic Tail of HIV-1 gp41 Protein.
Authors: Murphy, R.E. / Samal, A.B. / Vlach, J. / Saad, J.S.
History
DepositionMay 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 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: Cytoplasmic tail of HIV-1 gp41 protein


Theoretical massNumber of molelcules
Total (without water)12,3991
Polymers12,3991
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10930 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Cytoplasmic tail of HIV-1 gp41 protein


Mass: 12398.524 Da / Num. of mol.: 1 / Fragment: tail residues 750-854
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6TAN6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic13D HNCO
123isotropic13D HN(CA)CB
133isotropic13D HN(CO)CA
143isotropic13D HNCA
152isotropic12D 1H-15N HSQC
163isotropic13D (H)CCH-TOCSY
173isotropic13D CBCA(CO)NH
182isotropic13D 1H-15N NOESY
192isotropic13D 1H-15N TOCSY
1103isotropic12D 1H-13C HSQC aromatic
1113isotropic12D 1H-13C HSQC aliphatic
1121isotropic12D 1H-1H TOCSY
1131isotropic12D 1H-1H NOESY
1143isotropic13D 1H-13C HMQC NOESY
NMR detailsText: The author states that the unusual shifts in the 15N dimension are due to the high temperature at which the experiments were conducted

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle1500 uM gp4CTc, 50 mM sodium phosphate, 50 mM sodium chloride, 1 mM TCEP, 25 mM DPC, 95% H2O/5% D2Onatural abundance95% H2O/5% D2O
micelle2500 uM [U-99% 15N] gp4CTc, 50 mM sodium phosphate, 50 mM sodium chloride, 1 mM TCEP, 25 mM DPC, 95% H2O/5% D2O15N_sample95% H2O/5% D2O
micelle3500 uM [U-99% 13C; U-99% 15N] gp4CTc, 50 mM sodium phosphate, 50 mM sodium chloride, 1 mM TCEP, 25 mM DPC, 95% H2O/5% D2O13C_15N_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMgp4CTcnatural abundance1
50 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
1 mMTCEPnatural abundance1
25 mMDPCnatural abundance1
500 uMgp4CTc[U-99% 15N]2
50 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
1 mMTCEPnatural abundance2
25 mMDPCnatural abundance2
500 uMgp4CTc[U-99% 13C; U-99% 15N]3
50 mMsodium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
1 mMTCEPnatural abundance3
25 mMDPCnatural abundance3
Sample conditionsIonic strength: 200 mM / Label: conditions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 324 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 700 MHz / Details: triple resonance cryo-probe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Analysis2.4.2CCPNdata analysis
Analysis2.4.2CCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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