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- PDB-6v4t: MPER-TMD of HIV-1 Env bound with the entry inhibitor S2C3 -

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Basic information

Entry
Database: PDB / ID: 6v4t
TitleMPER-TMD of HIV-1 Env bound with the entry inhibitor S2C3
ComponentsEnvelope glycoprotein gp160
KeywordsVIRAL PROTEIN / HIV-1 Env / small-molecule / entry inhibitor / MPER
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 / 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
Chem-QOJ / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing
AuthorsXiao, T. / Frey, G. / Fu, Q. / Lavine, C.L. / Scott, D.A. / Seaman, M.S. / Chou, J.J. / Chen, B.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI129721 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127193 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI112489 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI141002 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI106488 United States
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: HIV-1 fusion inhibitors targeting the membrane-proximal external region of Env spikes.
Authors: Xiao, T. / Frey, G. / Fu, Q. / Lavine, C.L. / Scott, D.A. / Seaman, M.S. / Chou, J.J. / Chen, B.
History
DepositionNov 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: 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 1.2Jun 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 2.0May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _database_2.pdbx_DOI / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0646
Polymers18,5383
Non-polymers1,5263
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 100structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein Envelope glycoprotein gp160


Mass: 6179.373 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q74849
#2: Chemical ChemComp-QOJ / 4,4'-(decane-1,10-diyl)bis(9-amino-2,3-dihydro-1H-cyclopenta[b]quinolin-4-ium)


Mass: 508.740 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H44N4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic12D 1H-15N TROSY-HSQC

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Sample preparation

DetailsType: solution
Contents: 0.6 mM [U-99% 13C; U-99% 15N] MPER-TMD, 2 mM S2C3, 40 mM MOPS, 50 mM DMPC, 100 mM DHPC, 90% H2O/10% D2O
Label: MPERTMD/S2C3 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMMPER-TMD[U-99% 13C; U-99% 15N]1
2 mMS2C3natural abundance1
40 mMMOPSnatural abundance1
50 mMDMPCnatural abundance1
100 mMDHPCnatural abundance1
Sample conditionsIonic strength: 0.04 mM / Label: condition1 / pH: 6.8 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 14

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