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- PDB-2az2: Flock House virus B2-dsRNA Complex (P4122) -

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Basic information

Entry
Database: PDB / ID: 2az2
TitleFlock House virus B2-dsRNA Complex (P4122)
Components
  • 5'-R(*GP*CP*AP*(5BU)P*GP*GP*AP*CP*GP*CP*GP*(5BU)P*CP*CP*AP*(5BU)P*GP*C)-3'
  • B2 protein
KeywordsViral protein/RNA / protein-rna complex / four-helix bundle / Viral protein-RNA COMPLEX
Function / homology
Function and homology information


host cell mitochondrion / 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
RNA / RNA (> 10) / Protein B2
Similarity search - Component
Biological speciesFlock house virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChao, J.A. / Lee, J.H. / Chapados, B.R. / Debler, E.W. / Schneemann, A. / Williamson, J.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Dual modes of RNA-silencing suppression by Flock House virus protein B2.
Authors: Chao, J.A. / Lee, J.H. / Chapados, B.R. / Debler, E.W. / Schneemann, A. / Williamson, J.R.
History
DepositionSep 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-R(*GP*CP*AP*(5BU)P*GP*GP*AP*CP*GP*CP*GP*(5BU)P*CP*CP*AP*(5BU)P*GP*C)-3'
D: 5'-R(*GP*CP*AP*(5BU)P*GP*GP*AP*CP*GP*CP*GP*(5BU)P*CP*CP*AP*(5BU)P*GP*C)-3'
A: B2 protein
B: B2 protein


Theoretical massNumber of molelcules
Total (without water)28,0734
Polymers28,0734
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.625, 69.625, 154.633
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: RNA chain 5'-R(*GP*CP*AP*(5BU)P*GP*GP*AP*CP*GP*CP*GP*(5BU)P*CP*CP*AP*(5BU)P*GP*C)-3'


Mass: 6000.171 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein B2 protein


Mass: 8036.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flock house virus / Genus: Alphanodavirus / Gene: B2 / Production host: Escherichia coli (E. coli) / References: UniProt: P68831
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPEG 5K, ammomnium sulfate, sodium chloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9191 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2005
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9191 Å / Relative weight: 1
ReflectionResolution: 2.6→35.6 Å / Num. obs: 12367 / % possible obs: 100 % / Observed criterion σ(F): 0.008 / Observed criterion σ(I): 2
Reflection shellResolution: 2.6→2.74 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→35.6 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.265 850 RANDOM
Rwork0.245 --
all0.246 12360 -
obs0.246 12323 -
Refinement stepCycle: LAST / Resolution: 2.6→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1072 768 0 21 1861
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.2

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