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- PDB-6b3u: Solution Structure of HIV-1 GP41 Transmembrane Domain in Bicelles -

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Basic information

Entry
Database: PDB / ID: 6b3u
TitleSolution Structure of HIV-1 GP41 Transmembrane Domain in Bicelles
ComponentsHIV-1 GP41 Transmembrane Domain
KeywordsMEMBRANE PROTEIN / HIV-1 / Transmembrane domain / GP41 / solution structure / residual dipolar couplings
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 / 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
AuthorsChiliveri, S.C. / Louis, J.M. / Ghirlando, R. / Baber, J.L. / Bax, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK075023-08 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Tilted, Uninterrupted, Monomeric HIV-1 gp41 Transmembrane Helix from Residual Dipolar Couplings.
Authors: Chiliveri, S.C. / Louis, J.M. / Ghirlando, R. / Baber, J.L. / Bax, A.
History
DepositionSep 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 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 1.3May 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: HIV-1 GP41 Transmembrane Domain


Theoretical massNumber of molelcules
Total (without water)4,6511
Polymers4,6511
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4320 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 60structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide HIV-1 GP41 Transmembrane Domain


Mass: 4650.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Polypeptide sequence for the solution structure corresponds to GP160 (677-716; HXB2 numbering).
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Escherichia coli BL21(DE3) (bacteria) / 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 HNCO
121isotropic13D HNCA
131isotropic13D 1H-15N NOESY
141isotropic12D TROSY
151isotropic12D ARTSY
162anisotropic12D ARTSY
173anisotropic12D ARTSY
184anisotropic22D ARTSY
195isotropic22D ARTSY
1106isotropic22D TROSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
bicelle1500 uM [U-100% 13C; U-100% 15N; U-100% 2H] HIV-1 GP41 Transmembrane domain, 93% H2O/7% D2O500uM TM in 150mM DMPC/DHPC (q=0.4), 25mM MES (pH6.5)Backbone assignments93% H2O/7% D2O
gel solid2100 uM [U-100% 15N; 80%-2H] HIV-1 GP41 Transmembrane domain, 93% H2O/7% D2O100uM TM in 100mM DMPC/DHPC (q=0.4), 25mM MES (pH6.5) Polyacrylamide gel made with 1.4% (w/v) (3-Acrylamidopropyl)-trimethylammonium chloridePositive charged gel93% H2O/7% D2O
gel solid3100 uM [U-100% 15N; 80%-2H] HIV-1 GP41 Transmembrane domain, 93% H2O/7% D2O100uM TM in 100mM DMPC/DHPC (q=0.4), 25mM MES (pH6.5) Neutral polyacrylamide gelNeutral charged gel93% H2O/7% D2O
bicelle440 uM [U-100% 15N; U-80% 2H] HIV-1 GP41 Transmembrane domain, 93% H2O/7% D2OTM R707C-ThuliumDOTAM8 in 100mM DMPC/DHPC (q=0.4), 25mM MES (pH6.5)TM R707C Thulium93% H2O/7% D2O
bicelle570 uM [U-100% 15N; U-80% 2H] HIV-1 GP41 Transmembrane domain, 93% H2O/7% D2OTM R707C-LutetiumDOTAM8 in 100mM DMPC/DHPC (q=0.4), 25mM MES (pH6.5)TM R707C Lutetium93% H2O/7% D2O
bicelle6300 uM [U-100% 15N; U-80% 2H] HIV-1 GP41 Transmembrane domain, 93% H2O/7% D2O100uM 15N-TM and 200uM 14NTM-R707C in 100mM DMPC/DHPC (q=0.4), 25mM MES (pH6.5)Mixed labeled TM93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMHIV-1 GP41 Transmembrane domain[U-100% 13C; U-100% 15N; U-80% 2H]1
100 uMHIV-1 GP41 Transmembrane domain[U-100% 15N; 80%-2H]2
100 uMHIV-1 GP41 Transmembrane domain[U-100% 15N; 80%-2H]3
40 uMHIV-1 GP41 Transmembrane domain[U-100% 15N; U-80% 2H]4
70 uMHIV-1 GP41 Transmembrane domain[U-100% 15N; U-80% 2H]5
300 uMHIV-1 GP41 Transmembrane domain[U-100% 15N; U-80% 2H]6
Sample conditionsIonic strength: 25 mM / Label: ambient / pH: 6.5 / Pressure: 1 bar / Temperature: 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II9001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
CcpNMRCCPNchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 15

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