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- PDB-6e8w: MPER-TM Domain of HIV-1 envelope glycoprotein (Env) -

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Basic information

Entry
Database: PDB / ID: 6e8w
TitleMPER-TM Domain of HIV-1 envelope glycoprotein (Env)
ComponentsEnvelope glycoprotein gp160
KeywordsVIRAL PROTEIN / MPER-TMD HIV-1 Env gp41
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
AuthorsFu, Q. / Shaik, M.M. / Cai, Y. / Ghantous, F. / Piai, A. / Peng, H. / Rits-Volloch, S. / Liu, Z. / Harrison, S.C. / Seaman, M.S. ...Fu, Q. / Shaik, M.M. / Cai, Y. / Ghantous, F. / Piai, A. / Peng, H. / Rits-Volloch, S. / Liu, Z. / Harrison, S.C. / Seaman, M.S. / Chen, B. / 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: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure of the membrane proximal external region of HIV-1 envelope glycoprotein.
Authors: Fu, Q. / Shaik, M.M. / Cai, Y. / Ghantous, F. / Piai, A. / Peng, H. / Rits-Volloch, S. / Liu, Z. / Harrison, S.C. / Seaman, M.S. / Chen, B. / Chou, J.J.
History
DepositionJul 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 18, 2019Group: 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 1.4Jun 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
Revision 1.5May 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)18,5383
Polymers18,5383
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3680 Å2
ΔGint-26 kcal/mol
Surface area14250 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 150structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Envelope glycoprotein gp160


Mass: 6179.373 Da / Num. of mol.: 3 / Fragment: Helical transmembrane residues 653-703
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Plasmid: pMM - LR6 / Details (production host): fused to C-terminus of the trpLE / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / 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
111isotropic32D 1H-15N TROSY HSQC
122isotropic33D HNCA
132isotropic33D HN(CO)CA
142isotropic33D HNCO
153isotropic23D 1H-15N NOESY tr-HSQC
193isotropic23D 1H-13C NOESY
184isotropic13D 1H-15N NOESY tr-HSQC
174isotropic13D 1H-13C NOESY
165isotropic13D Jch MODULATED 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
bicelle115N, 2H Envelope glycoprotein gp160, 50 mM DMPC, 100 mM DHPC, 90% H2O/10% D2O15N, 2H90% H2O/10% D2O
bicelle215N, 2H, 13C Envelope glycoprotein gp160, 50 mM DMPC, 100 mM DHPC, 90% H2O/10% D2O15N, 2H, 13C90% H2O/10% D2O
bicelle315N, 13C Envelope glycoprotein gp160, 50 mM [U-99% 2H] DMPC, 100 mM [U-99% 2H] DHPC, 90% H2O/10% D2O15N, 13C90% H2O/10% D2O
bicelle415N, 2H mixed with 13C(15%) Envelope glycoprotein gp160, 50 mM [U-99% 2H] DMPC, 100 mM [U-99% 2H] DHPC, 90% H2O/10% D2O15N, 2H mixed with 13C(15%)90% H2O/10% D2O
bicelle515N, 2H mixed with 13C Envelope glycoprotein gp160, 50 mM [U-99% 2H] DMPC, 100 mM [U-99% 2H] DHPC, 90% H2O/10% D2O15N, 2H mixed with 13C90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMDMPCnatural abundance1
100 mMDHPCnatural abundance1
50 mMDMPCnatural abundance2
100 mMDHPCnatural abundance2
50 mMDMPC[U-99% 2H]3
100 mMDHPC[U-99% 2H]3
50 mMDMPC[U-99% 2H]4
100 mMDHPC[U-99% 2H]4
50 mMDMPC[U-99% 2H]5
100 mMDHPC[U-99% 2H]5
Envelope glycoprotein gp16015N, 2H1
Envelope glycoprotein gp160[U-13C; U-15N; U-2H]2
Envelope glycoprotein gp160[U-100% 13C; U-100% 15N]3
Envelope glycoprotein gp16015N, 2H mixed with 13C(15%)4
Envelope glycoprotein gp16015N, 2H mixed with 13C5
Sample conditionsIonic strength: 20 mM / Label: Bicelle / pH: 6.7 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9002
Bruker AVANCE IIBrukerAVANCE II8001
Bruker AVANCE IIBrukerAVANCE II6003

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Processing

NMR software
NameVersionDeveloperClassification
XEASYBartels et al.chemical shift assignment
X-PLOR NIH2.48Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
X-PLOR NIH2.48Schwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 15

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