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- PDB-5jyn: Structure of the transmembrane domain of HIV-1 gp41 in bicelle -

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Basic information

Entry
Database: PDB / ID: 5jyn
TitleStructure of the transmembrane domain of HIV-1 gp41 in bicelle
ComponentsEnvelope glycoprotein gp160
KeywordsVIRAL PROTEIN / transmembrane domain / lipid bilayer / transmembrane trimer
Function / homology
Function and homology information


host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / 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
AuthorsDev, J. / Fu, Q. / Park, D. / Chen, B. / Chou, J.J.
Funding support United States, China, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL103526 United States
CASXDB08030301 China
CitationJournal: Science / Year: 2016
Title: Structural basis for membrane anchoring of HIV-1 envelope spike.
Authors: Dev, J. / Park, D. / Fu, Q. / Chen, J. / Ha, H.J. / Ghantous, F. / Herrmann, T. / Chang, W. / Liu, Z. / Frey, G. / Seaman, M.S. / Chen, B. / Chou, J.J.
History
DepositionMay 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Structure summary
Category: citation / entity / pdbx_audit_support
Item: _citation.journal_id_CSD / _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 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
Revision 1.6May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein gp160
B: Envelope glycoprotein gp160
C: Envelope glycoprotein gp160


Theoretical massNumber of molelcules
Total (without water)13,9523
Polymers13,9523
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3740 Å2
ΔGint-31 kcal/mol
Surface area9870 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Envelope glycoprotein gp160


Mass: 4650.604 Da / Num. of mol.: 3 / Fragment: GP41 domain residues 670-709
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q74849

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D TROSY HNCA
121isotropic13D TROSY HN(CO)CA
131isotropic13D TROSY HN(CA)CO
141isotropic13D TROSY HNCO
152isotropic33D 15N NOESY-TROSY-HSQC
162isotropic33D 13C NOESY-HSQC (Methyls)
173isotropic23D 15N NOESY-TROSY-HSQC (long mixing time)
181isotropic12D 15N TROSY-HSQC for GdDOTA titration
194isotropic13D 15N NOESY-TROSY-HSQC (short mixing time)

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
bicelle10.8 mM [U-13C; U-15N; 85%-2H] HIV-1 gp41 Transmembrane Domain, 60 mM regular 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 120 mM regular 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), 25 mM regular MES, 0.1 % regular NaN3, 95% H2O/5% D2OFor assignment of protein backbone resonancestriple labeled sample95% H2O/5% D2O
bicelle20.8 mM [U-13C; U-15N] HIV-1 gp41 Transmembrane Domain, 60 mM acyl chains 2H labeled 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 120 mM acyl chains 2H labeled 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), 25 mM regular MES, 0.1 % regular NaN3, 95% H2O/5% D2OFor recording 3D 15N-edited and 13C-edited NOESYsdouble labeled sample95% H2O/5% D2O
bicelle30.4 mM [U-15N; U-2H] HIV-1 gp41 Transmembrane Domain, 0.4 mM [15% 13C] HIV-1 gp41 Transmembrane Domain, 60 mM acyl chains 2H labeled 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 120 mM acyl chains 2H labeled 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), 25 mM regular MES, 0.1 % regular NaN3, 95% H2O/5% D2OFor assigning inter-molecular NOEsmixed labeled sample95% H2O/5% D2O
bicelle40.8 mM [U-15N] HIV-1 gp41 Transmembrane Domain, 60 mM acyl chains 2H labeled 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 120 mM acyl chains 2H labeled 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), 25 mM regular MES, 0.1 % regular NaN3, 95% H2O/5% D2OFor assigning Arg sidechains15N labeled sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMHIV-1 gp41 Transmembrane Domain[U-13C; U-15N; 85%-2H]1
60 mM1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)regular1
120 mM1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)regular1
25 mMMESregular1
0.1 %NaN3regular1
0.8 mMHIV-1 gp41 Transmembrane Domain[U-13C; U-15N]2
60 mM1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)acyl chains 2H labeled2
120 mM1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)acyl chains 2H labeled2
25 mMMESregular2
0.1 %NaN3regular2
0.4 mMHIV-1 gp41 Transmembrane Domain-1[U-15N; U-2H]3
0.4 mMHIV-1 gp41 Transmembrane Domain-2[15% 13C]3
60 mM1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)acyl chains 2H labeled3
120 mM1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)acyl chains 2H labeled3
25 mMMESregular3
0.1 %NaN3regular3
0.8 mMHIV-1 gp41 Transmembrane Domain[U-15N]4
60 mM1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)acyl chains 2H labeled4
120 mM1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)acyl chains 2H labeled4
25 mMMESregular4
0.1 %NaN3regular4
Sample conditionsIonic strength: 50 mM / Ionic strength err: 10 / Label: ambient / pH: 6.7 / PH err: 0.1 / Pressure: 1 atm / Temperature: 303 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIBrukerAVANCE II6001cryogenic probe
Bruker AVANCE IIBrukerAVANCE II7502cryogenic probe
Bruker AVANCE IIIBrukerAVANCE III9003cryogenic probe

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Processing

NMR software
NameVersionDeveloperClassification
XPLOR-NIH2.42G. Marius Clore , Guillermo Bermejo, , John Kuszewski, Charles D. Schwieters, and Nico Tjandrastructure calculation
CcpNMRCCPNchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
TALOSCornilescu, Delaglio and Baxdata analysis
XPLOR-NIH2.42G. Marius Clore , Guillermo Bermejo, , John Kuszewski, Charles D. Schwieters, and Nico Tjandrarefinement
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 15

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