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- PDB-1mzi: Solution ensemble structures of HIV-1 gp41 2F5 mAb epitope -

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Basic information

Entry
Database: PDB / ID: 1mzi
TitleSolution ensemble structures of HIV-1 gp41 2F5 mAb epitope
Components2F5 epitope of HIV-1 gp41 fusion protein
KeywordsVIRAL PROTEIN / Ensemble / statistics
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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
MethodSOLUTION NMR / Ensemble generation with MEDUSA, Clustering analysis with NMRCLUST, Statistical analysis of the ensemble with NAMFIS
AuthorsBarbato, G. / Bianchi, E. / Ingallinella, P. / Hurni, W.H. / Miller, M.D. / Ciliberto, G. / Cortese, R. / Bazzo, R. / Shiver, J.W. / Pessi, A.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Structural analysis of the epitope of the anti-HIV antibody 2F5 sheds light into its mechanism of neutralization and HIV fusion.
Authors: Barbato, G. / Bianchi, E. / Ingallinella, P. / Hurni, W.H. / Miller, M.D. / Ciliberto, G. / Cortese, R. / Bazzo, R. / Shiver, J.W. / Pessi, A.
#1: Journal: J.Biomol.NMR / Year: 1991
Title: Multi-conformational peptide dynamics derived from NMR data: a new search algorithm and its application to antamanide
Authors: Bruschweiler, R. / Blackledge, M. / Ernst, R.R.
#2: Journal: J.Am.Chem.Soc. / Year: 1995
Title: NMR analysis of molecular flexibility in solution: a new method for the study of complex distributions of rapidly exchanging conformations. Application to a 13-residue peptide with an 8-residue loop
Authors: Cicero, D.O. / Barbato, G. / Bazzo, R.
#3: Journal: Protein Eng. / Year: 1996
Title: An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies
Authors: Kelley, L.A. / Gardner, S.P. / Sutcliffe, M.J.
History
DepositionOct 8, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 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: 2F5 epitope of HIV-1 gp41 fusion protein


Theoretical massNumber of molelcules
Total (without water)1,6181
Polymers1,6181
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)81 / 6400Base set ensemble representative of the conformational space experimentally allowed
Representative

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Components

#1: Protein/peptide 2F5 epitope of HIV-1 gp41 fusion protein / Envelope polyprotein GP160


Mass: 1617.820 Da / Num. of mol.: 1 / Fragment: 13 residues 2F5 epitope / Source method: obtained synthetically / Details: GP160 HIV-1 HBX2 isolate amino acids 659-671 / References: UniProt: P04578

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131PE-COSY
141HSQC (1H-13C)-Dipsi-2(1H)
151HMQC (1H-15N) jr
NMR detailsText: Distance restraints were determined using NOESY build-up curves. The coupling constants were determined using phase sensitive COSY and TOCSY experiments. E threshold cutoff and deltaE allowance ...Text: Distance restraints were determined using NOESY build-up curves. The coupling constants were determined using phase sensitive COSY and TOCSY experiments. E threshold cutoff and deltaE allowance for MEDUSA were 600 and 100 kCal/mol respectively Clustering was performed with a cutoff of 1.0Angstrom A conformer was defined as different if either phi or psi angle for at least one aminoacid was differing by >15 degrees

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM peptide, 50mM phosphate buffer, pH 6.595% H2O/5% D2O
21.5mM peptide, 50mM phosphate buffer, pH 6.5100% D2O
Sample conditionsIonic strength: 50mM phosphate buffer / pH: 6.5 / Pressure: ambient / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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 DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2001Delaglio, F.data analysis
NMRView2001Johnson, B.data analysis
DGIIMSIMSI, Increfinement
NAMFIS1Cicero D.refinement
MEDUSAin homeBrushweiler R.refinement
NMRCLUST1.2Kelleyrefinement
RefinementMethod: Ensemble generation with MEDUSA, Clustering analysis with NMRCLUST, Statistical analysis of the ensemble with NAMFIS
Software ordinal: 1
NMR ensembleConformer selection criteria: Base set ensemble representative of the conformational space experimentally allowed
Conformers calculated total number: 6400 / Conformers submitted total number: 81

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