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- PDB-2nct: NMR assignment and structure of a peptide derived from the membra... -

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Basic information

Entry
Database: PDB / ID: 2nct
TitleNMR assignment and structure of a peptide derived from the membrane proximal external region of HIV-1 gp41 in the presence of hexafluoroisopropanol
ComponentsEnvelope glycoprotein gp41
KeywordsVIRAL PROTEIN / neutralizing epitope / peptide vaccine
Function / homologyRetroviral envelope protein / Retroviral envelope protein GP41-like / viral envelope / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane / Env polyprotein
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsJimenez, M. / Nieva, J.L. / Rujas, E. / Partida-Hanon, A. / Bruix, M.
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis for broad neutralization of HIV-1 through the molecular recognition of 10E8 helical epitope at the membrane interface.
Authors: Rujas, E. / Caaveiro, J.M. / Partida-Hanon, A. / Gulzar, N. / Morante, K. / Apellaniz, B. / Garcia-Porras, M. / Bruix, M. / Tsumoto, K. / Scott, J.K. / Jimenez, M.A. / Nieva, J.L.
History
DepositionApr 14, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein gp41


Theoretical massNumber of molelcules
Total (without water)4,6251
Polymers4,6251
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Envelope glycoprotein gp41


Mass: 4624.687 Da / Num. of mol.: 1 / Fragment: UNP residues 95-121 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q66X49

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
2322D 1H-1H TOCSY
2422D 1H-1H NOESY
1522D 1H-13C HSQC aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM 10E8p, 25 % v/v [U-2H] HFIP, 2 mM HEPES, 0.1 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM 10E8p, 25 % v/v [U-2H] HFIP, 2 mM HEPES, 0.1 mM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mM10E8p-11
0.25 v/vHFIP-2[U-2H]1
2 mMHEPES-31
0.1 mMDSS-41
0.5 mM10E8p-52
0.25 v/vHFIP-6[U-2H]2
2 mMHEPES-72
0.1 mMDSS-82
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
12 7 ambient 308 K
22 7 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdihedral angle restraints
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 361 / NOE intraresidue total count: 182 / NOE medium range total count: 82 / NOE sequential total count: 97 / Protein phi angle constraints total count: 29 / Protein psi angle constraints total count: 29
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.001 Å / Distance rms dev error: 0 Å

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