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- PDB-2jnr: Discovery and optimization of a natural HIV-1 entry inhibitor tar... -

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Basic information

Entry
Database: PDB / ID: 2jnr
TitleDiscovery and optimization of a natural HIV-1 entry inhibitor targeting the gp41 fusion peptide
Components
  • ENV polyproteinEnv (gene)
  • VIR165
KeywordsVIRAL PROTEIN / Peptide complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / 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 speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
Model detailsComplex of VIR165 and FP1-23
Model type detailsminimized average
AuthorsMunch, J. / Standker, L. / Adermann, K. / Schulz, A. / Pohlmann, S. / Chaipan, C. / Biet, T. / Peters, T. / Meyer, B. / Wilhelm, D. ...Munch, J. / Standker, L. / Adermann, K. / Schulz, A. / Pohlmann, S. / Chaipan, C. / Biet, T. / Peters, T. / Meyer, B. / Wilhelm, D. / Lu, H. / Jing, W. / Jiang, S. / Forssmann, W. / Kirchhoff, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Discovery and Optimization of a Natural HIV-1 Entry Inhibitor Targeting the gp41 Fusion Peptide.
Authors: Munch, J. / Standker, L. / Adermann, K. / Schulz, A. / Schindler, M. / Chinnadurai, R. / Pohlmann, S. / Chaipan, C. / Biet, T. / Peters, T. / Meyer, B. / Wilhelm, D. / Lu, H. / Jing, W. / ...Authors: Munch, J. / Standker, L. / Adermann, K. / Schulz, A. / Schindler, M. / Chinnadurai, R. / Pohlmann, S. / Chaipan, C. / Biet, T. / Peters, T. / Meyer, B. / Wilhelm, D. / Lu, H. / Jing, W. / Jiang, S. / Forssmann, W.G. / Kirchhoff, F.
History
DepositionFeb 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Remark 999 SEQUENCE The author states that VIR-165 is a modified form of VIRus-Inhibitory Peptide, VIRIP ... SEQUENCE The author states that VIR-165 is a modified form of VIRus-Inhibitory Peptide, VIRIP which corresponds exactly to residues 353-372 of human alpha1-antitrypsin (UNP entry P01009). VIR-165 (LEAIPCSIPPCFAFNKPFVF) differs from VIRIP (LEAIPMSIPPEVKFNKPFVF) by three amino acid changes that enhance its ability to inhibit infection by human immunodeficiency virus type 1 (HIV-1).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VIR165
B: ENV polyprotein


Theoretical massNumber of molelcules
Total (without water)4,3672
Polymers4,3672
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1all calculated structures submitted
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide VIR165


Mass: 2241.689 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: VIR-165 is a modified form of the VIRus-Inhibitory Peptide (VIRIP) which naturally occurs in human plasma.
Source: (synth.) synthetic construct (others)
#2: Protein/peptide ENV polyprotein / Env (gene) / FP1-23


Mass: 2125.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q72502

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Complex of VIR165 and FP1-23
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D DQF-COSY
1312D 1H-1H TOCSY

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Sample preparation

DetailsContents: 0.75 mM VIR165, 0.75 mM FP1-23, 3%DMSO added, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.75 mMVIR1651
0.75 mMFP1-231
Sample conditionsIonic strength: 0 / pH: 4.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX7001
Bruker DRXBrukerDRX5002
Bruker DPXBrukerDPX2503

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Processing

NMR softwareName: SYBYL / Developer: Tripos / Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 1 / Conformers submitted total number: 1

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