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- PDB-2pv6: HIV-1 gp41 Membrane Proximal Ectodomain Region peptide in DPC micelle -

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Basic information

Entry
Database: PDB / ID: 2pv6
TitleHIV-1 gp41 Membrane Proximal Ectodomain Region peptide in DPC micelle
ComponentsEnvelope glycoprotein
KeywordsVIRAL PROTEIN / kinked helix
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / Alpha-defensins / Dectin-2 family / positive regulation of establishment of T cell polarity / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / Alpha-defensins / Dectin-2 family / positive regulation of establishment of T cell polarity / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / : / viral envelope / apoptotic process / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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
AuthorsSun, Z.-Y.J. / Oh, K.J. / Kim, M. / Reinherz, E.L. / Wagner, G.
CitationJournal: Immunity / Year: 2008
Title: HIV-1 broadly neutralizing antibody extracts its epitope from a kinked gp41 ectodomain region on the viral membrane
Authors: Sun, Z.Y. / Oh, K.J. / Kim, M. / Yu, J. / Brusic, V. / Song, L. / Qiao, Z. / Wang, J.H. / Wagner, G. / Reinherz, E.L.
History
DepositionMay 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)2,9291
Polymers2,9291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 20structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Envelope glycoprotein / Env polyprotein


Mass: 2929.330 Da / Num. of mol.: 1 / Fragment: residues 662-683
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: HXB2 / Gene: env
Plasmid details: peptide cleaved from N-terminal GB1-fusioned construct by CNBr
Plasmid: pET30a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04578

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111triple resonance backbone experiments
1213D 13C-separated NOESY
1323D 15N-separated NOESY
1432D NOESY
151HNHA
161HNHB
1723D 15N-separated N(H)-NH NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM U-15N,13C MPER + 100mM d38 DPC, 90% H2O/10% D2O90% H2O/10% D2O
21mM U-15N MPER + 100mM d38 DPC, 90% H2O/10% D2O90% H2O/10% D2O
31mM unlabeled MPER + 100mM d38 DPC, 100% D2O100% D2O
Sample conditionsIonic strength: no salt / pH: 6.6 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7501
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE5003
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
PROSA6Guntertprocessing
CARA1.8.2Kellerdata analysis
CYANA2.1Guntertstructure solution
X-PLORxplor-nih-2.9.7Brunger, Schwietersstructure solution
TALOS2003.027.13.05Cornilescudata analysis
X-PLORxplor-nih-2.9.7Brunger, Schwietersrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 331 NOE restraints, 10 hydrogen bond constraints, and 34 dihydral angle restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 17

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