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- PDB-2b9z: Solution structure of FHV B2, a viral suppressor of RNAi -

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Basic information

Entry
Database: PDB / ID: 2b9z
TitleSolution structure of FHV B2, a viral suppressor of RNAi
ComponentsB2 protein
KeywordsVIRAL PROTEIN / Symmetric antiparallel homodimer / all alpha-helical
Function / homology
Function and homology information


host cell mitochondrion / virus-mediated perturbation of host defense response / RNA binding
Similarity search - Function
RNA-binding protein, B2 / RNA-binding protein B2 superfamily / RNA binding protein B2 / ESAT-6-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesFlock house virus
MethodSOLUTION NMR / molecular dynamics, simulated annealing
AuthorsLingel, A. / Simon, B. / Izaurralde, E. / Sattler, M.
CitationJournal: Embo Rep. / Year: 2005
Title: The structure of the flock house virus B2 protein, a viral suppressor of RNA interference, shows a novel mode of double-stranded RNA recognition.
Authors: Lingel, A. / Simon, B. / Izaurralde, E. / Sattler, M.
History
DepositionOct 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2005Provider: 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 ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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.deposit_site / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 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: B2 protein
B: B2 protein


Theoretical massNumber of molelcules
Total (without water)16,1272
Polymers16,1272
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein B2 protein


Mass: 8063.382 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flock house virus / Genus: Alphanodavirus / Gene: B2 / Plasmid: pETM-11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P68831

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
131HNHA
NMR detailsText: Distance restraints were derived from 15N- or 13C-resolved 3D NOESY. HN-N residual dipolar couplings were measured using a spin-state-selective 1H,15N correlation experiment in dilute liquid ...Text: Distance restraints were derived from 15N- or 13C-resolved 3D NOESY. HN-N residual dipolar couplings were measured using a spin-state-selective 1H,15N correlation experiment in dilute liquid crystalline medium. Restraints for the backbone angles phi and psi were derived from TALOS. Stereospecific assignments of Leu, Val methyl groups were obtained using a 10% fractionally 13C-labelled sample.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2 - 1 mM 15N, 13C/15N or 2H/13C/15N labelled B2 protein in 50 mM sodium phosphate pH 6.3, 50 mM sodium chloride, 1 mM DTT, 90% H2O / 10% D2O90% H2O/10% D2O
20.2 - 1 mM 13C/15N labelled B2 protein in 50 mM sodium phosphate pH 6.3, 50 mM sodium chloride, 1 mM DTT, 100% D2O100% D2O
Sample conditionsIonic strength: 50 mM NaPi, 50 mM NaCl / pH: 6.3 / Pressure: 1 atm / Temperature: 295 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 DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX9003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5collection
NMRPipeDelaglio et al.processing
NMRView5Johnson et al.data analysis
TALOSCornilescu et al.data analysis
ARIA1.2Linge et al.structure solution
CNS1.1Brunger et al.structure solution
CNS1.1Brunger et al.refinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
Details: The experimentally determined distance, dihedral and dipolar coupling restraints were applied in a simulated annealing protocol using ARIA and CNS. Non-crystallographic symmetry (NCS) ...Details: The experimentally determined distance, dihedral and dipolar coupling restraints were applied in a simulated annealing protocol using ARIA and CNS. Non-crystallographic symmetry (NCS) restraints were used to enforce the dimer symmetry. The final ensemble of NMR structures was refined in a shell of water molecules.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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