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- PDB-7loh: Structure of the HIV-1 gp41 transmembrane domain and cytoplasmic tail -

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Basic information

Entry
Database: PDB / ID: 7loh
TitleStructure of the HIV-1 gp41 transmembrane domain and cytoplasmic tail
ComponentsTransmembrane protein gp41Transmembrane protein
KeywordsMEMBRANE PROTEIN / MPER / TMD / CT / Membrane-proximal external region / Transmembrane domain / Cytoplasmic tail
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / 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
AuthorsPiai, A. / Fu, Q. / Sharp, A.K. / Bighi, B. / Brown, A.M. / Chou, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127193 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: NMR Model of the Entire Membrane-Interacting Region of the HIV-1 Fusion Protein and Its Perturbation of Membrane Morphology.
Authors: Piai, A. / Fu, Q. / Sharp, A.K. / Bighi, B. / Brown, A.M. / Chou, J.J.
History
DepositionFeb 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 19, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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: Transmembrane protein gp41
B: Transmembrane protein gp41
C: Transmembrane protein gp41


Theoretical massNumber of molelcules
Total (without water)62,5393
Polymers62,5393
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area12100 Å2
ΔGint-78 kcal/mol
Surface area37290 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 Transmembrane protein gp41 / Transmembrane protein / TM / Glycoprotein 41 / gp41


Mass: 20846.182 Da / Num. of mol.: 3 / Mutation: C764S, A823G, C837S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A386YSI0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N TROSY HSQC
121isotropic13D TROSY HNCO
131isotropic13D TROSY HNCA
142isotropic12D 1H-15N TROSY HSQC
152isotropic12D 1H-13C HSQC
162isotropic13D 15N-edited NOESY-TROSY-HSQC
172isotropic13D 13C-edited NOESY
182isotropic13D 15N-edited TROSY-NOESY-TROSY-HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
bicelle11.2 mM [U-100% 13C; U-100% 15N; U-85% 2H] HIV1 gp41 TMD-CT, 40 mM DMPC, 80 mM DHPC, 40 mM MES, 1 % sodium azide, 90% H2O/10% D2OTriple-labeled_sample90% H2O/10% D2O
bicelle21 mM [ILV-100% 13C; U-100% 15N; U-85% 2H] HIV1 gp41 TMD-CT, 40 mM DMPC, 80 mM DHPC, 40 mM MES, 1 % sodium azide, 90% H2O/10% D2OILV_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMHIV1 gp41 TMD-CT[U-100% 13C; U-100% 15N; U-85% 2H]1
40 mMDMPCnatural abundance1
80 mMDHPCnatural abundance1
40 mMMESnatural abundance1
1 %sodium azidenatural abundance1
1 mMHIV1 gp41 TMD-CT[ILV-100% 13C; U-100% 15N; U-85% 2H]2
40 mMDMPCnatural abundance2
80 mMDHPCnatural abundance2
40 mMMESnatural abundance2
1 %sodium azidenatural abundance2
Sample conditionsIonic strength: 0 M / Label: Conditions_1 / pH: 6.7 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichpeak picking
XEASYBartels et al.peak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 5
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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