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- PDB-2me1: HIV-1 gp41 clade B double alanine mutant Membrane Proximal Extern... -

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Basic information

Entry
Database: PDB / ID: 2me1
TitleHIV-1 gp41 clade B double alanine mutant Membrane Proximal External Region peptide in DPC micelle
ComponentsGp41
KeywordsMEMBRANE PROTEIN / MPER / viral fusion / helix-hinge-helix
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / 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 / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / 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
Model detailsclosest to the average, model1
AuthorsSun, Z.J. / Wagner, G. / Reinherz, E.L. / Kim, M. / Song, L. / Choi, J. / Cheng, Y. / Chowdhury, B. / Bellot, G. / Shih, W.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Disruption of Helix-Capping Residues 671 and 674 Reveals a Role in HIV-1 Entry for a Specialized Hinge Segment of the Membrane Proximal External Region of gp41.
Authors: Sun, Z.Y. / Cheng, Y. / Kim, M. / Song, L. / Choi, J. / Kudahl, U.J. / Brusic, V. / Chowdhury, B. / Yu, L. / Seaman, M.S. / Bellot, G. / Shih, W.M. / Wagner, G. / Reinherz, E.L.
History
DepositionSep 20, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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: Gp41


Theoretical massNumber of molelcules
Total (without water)3,4561
Polymers3,4561
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)10 / 30target function
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Gp41 / MPER-HxB2-AA


Mass: 3455.952 Da / Num. of mol.: 1
Fragment: membrane proximal external region (UNP residues 657-683)
Mutation: N671A/N674A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: clade B, HxB2 isolate / Gene: env / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / 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
1113D HNCO,HNCA,HN(CA)CB,HN(COCA)CB,HN(CO)CA,HN(CA)CO
1213D C(CO)NH,H(CCO)NH,(H)CCH-TOCSY
1313D 1H-13C NOESY
1423D 1H-15N NOESY
1523D HNHA
1632D 1H-1H NOESY,TOCSY
174Q-J RDC
NMR detailsText: MODELS SUPERIMPOSED FROM RESIDUE 666 TO RESIDUE 682.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] MPER-HXB2-AA, 100 mM [U-100% 2H] DPC, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] MPER-HXB2-AA, 100 mM [U-100% 2H] DPC, 90% H2O/10% D2O90% H2O/10% D2O
31 mM MPER-HXB2-AA, 100 mM [U-100% 2H] DPC, 100% D2O100% D2O
41 mM [U-100% 13C; U-100% 15N] MPER-HXB2-AA, 100 mM [U-100% 2H] DPC, 20 mg/mL DNA nanotube, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMPER-HXB2-AA-1[U-100% 13C; U-100% 15N]1
100 mMDPC-2[U-100% 2H]1
1 mMMPER-HXB2-AA-3[U-100% 15N]2
100 mMDPC-4[U-100% 2H]2
1 mMMPER-HXB2-AA-53
100 mMDPC-6[U-100% 2H]3
1 mMMPER-HXB2-AA-7[U-100% 13C; U-100% 15N]4
100 mMDPC-8[U-100% 2H]4
20 mg/mLDNA nanotube-94
Sample conditionsIonic strength: 0 / pH: 6.6 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE7502
Bruker AvanceBrukerAVANCE6003
Bruker AvanceBrukerAVANCE5004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARA1.8.4Rochus Kellerdata analysis
CARA1.8.4Rochus Kellerchemical shift assignment
CARA1.8.4Rochus Kellerpeak picking
TALOS+Shen, Cornilescu, Delaglio and Baxdata analysis
CYANA3.0cGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.28Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure models were calculated using TENSO module incorporating RDC restraints during the high temperature torsion angle dynamics annealing stage, and planeDisPot module incorporating EPR ...Details: Structure models were calculated using TENSO module incorporating RDC restraints during the high temperature torsion angle dynamics annealing stage, and planeDisPot module incorporating EPR depth restraints during the subsequent low temperature Cartesian coordinate dynamics annealing stage.
NMR constraintsNOE constraints total: 335 / NOE intraresidue total count: 159 / NOE long range total count: 6 / NOE medium range total count: 67 / NOE sequential total count: 103 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 25 / Protein psi angle constraints total count: 22
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 30 / Conformers submitted total number: 10 / Maximum torsion angle constraint violation: 4.1 ° / Maximum upper distance constraint violation: 0.29 Å

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