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- PDB-2hn8: Structural characterization and oligomerization of PB1-F2, a pro-... -

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Basic information

Entry
Database: PDB / ID: 2hn8
TitleStructural characterization and oligomerization of PB1-F2, a pro-apoptotic influenza A virus protein
ComponentsProtein PB1-F2
KeywordsVIRAL PROTEIN / pro-apoptotic mitochondrial targeting protein
Function / homology
Function and homology information


host cell mitochondrial inner membrane / Influenza Virus Induced Apoptosis / symbiont-mediated perturbation of host apoptosis / host cell cytosol / Viral mRNA Translation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / host cell nucleus / membrane
Similarity search - Function
Influenza A proapoptotic protein PB1-F2 / Influenza A Proapoptotic protein
Similarity search - Domain/homology
MethodSOLUTION NMR / simulated annealing
AuthorsBruns, K. / Studtrucker, N. / Sharma, A. / Fossen, T. / Mitzner, D. / Eissmann, A. / Tessmer, U. / Roder, R. / Henklein, P. / Wray, V. / Schubert, U.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural characterization and oligomerization of PB1-F2, a pro-apoptotic influenza A virus protein.
Authors: Bruns, K. / Studtrucker, N. / Sharma, A. / Fossen, T. / Mitzner, D. / Eissmann, A. / Tessmer, U. / Roder, R. / Henklein, P. / Wray, V. / Schubert, U.
History
DepositionJul 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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: Protein PB1-F2


Theoretical massNumber of molelcules
Total (without water)4,8491
Polymers4,8491
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)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Protein PB1-F2


Mass: 4848.931 Da / Num. of mol.: 1 / Fragment: C-terminal domain, amino acid residues 50-87 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally expressed/found in cells infected with Homo sapiens (human) Influenza A virus strain A/Puerto Rico/8/34 (H1N1).
References: UniProt: P0C0U1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2 mM PB(50-87), 300 K, pH 3, 50% H2O, 50% TFE-d2 / Solvent system: 50% H2O, 50% TFE-d2
Sample conditionsIonic strength: 0 / pH: 3 / Pressure: ambient / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenrefinement
CNS1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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