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- PDB-2imu: NMR structure of pep46 from the infectious bursal disease virus (... -

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Basic information

Entry
Database: PDB / ID: 2imu
TitleNMR structure of pep46 from the infectious bursal disease virus (IBDV) in dodecylphosphocholin (DPC).
ComponentsStructural polyprotein (PP) p1
KeywordsVIRAL PROTEIN / IBDV / p4 / BIRNAVIRUS / DPC / VP2 / PORE FORMATION
Function / homology
Function and homology information


T=13 icosahedral viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / host cell cytoplasm / structural molecule activity / proteolysis / identical protein binding / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1030 / Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1030 / Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Viral coat protein subunit
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
MethodSOLUTION NMR / distance geometry, simulated annealing, energy minimization
AuthorsGalloux, M. / Libersou, S. / Morellet, N. / Bouaziz, S. / Ouldali, M. / Da Costa, B. / Lepault, J. / Delmas, B.
CitationJournal: To be Published
Title: Cell entry of a dsRNA virus through pores induced by one of its structural peptides.
Authors: Galloux, M. / Libersou, S. / Morellet, N. / Bouaziz, S. / Ouldali, M. / Da Costa, B. / Lepault, J. / Delmas, B.
History
DepositionOct 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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: Structural polyprotein (PP) p1


Theoretical massNumber of molelcules
Total (without water)4,8821
Polymers4,8821
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)13 / 100structures with acceptable covalent geometry,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Structural polyprotein (PP) p1


Mass: 4881.651 Da / Num. of mol.: 1 / Fragment: IBDV pep46 / Source method: obtained synthetically
Details: This sequence occurs naturally in an infectious bursal disease virus (IBDV), an avian birnavirus.
References: UniProt: P61825

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 1mM pep46; 40mM DPC; 90%H2O, 10%D2O / Solvent system: 90%H20, 10%D2O
Sample conditionsIonic strength: 0 / pH: 3.5 / Pressure: 1 atm / Temperature: 333 K

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NMR measurement

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

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Processing

NMR software
NameVersionClassification
XwinNMR3collection
XwinNMR3processing
XwinNMR3data analysis
X-PLOR3.851structure solution
X-PLOR3.851refinement
RefinementMethod: distance geometry, simulated annealing, energy minimization
Software ordinal: 1
Details: The structures are based on 461 noe-derived distance constraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 13

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