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- PDB-1di2: CRYSTAL STRUCTURE OF A DSRNA-BINDING DOMAIN COMPLEXED WITH DSRNA:... -

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Basic information

Entry
Database: PDB / ID: 1di2
TitleCRYSTAL STRUCTURE OF A DSRNA-BINDING DOMAIN COMPLEXED WITH DSRNA: MOLECULAR BASIS OF DOUBLE-STRANDED RNA-PROTEIN INTERACTIONS
Components
  • DOUBLE STRANDED RNA BINDING PROTEIN A
  • RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / PROTEIN-RNA COMPLEX / DOUBLE STRANDED RNA / PROTEIN-RNA INTERACTIONS / RNA-BINING PROTEIN / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


siRNA processing / enzyme activator activity / double-stranded RNA binding / nucleolus / perinuclear region of cytoplasm / cytoplasm
Similarity search - Function
Interferon-inducible double-stranded RNA-dependent protein kinase activator A / PRKRA, first double-stranded RNA binding domain / PRKRA, second double-stranded RNA binding domain / PRKRA, third double-stranded RNA binding domain / Staufen, C-terminal / Staufen C-terminal domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. ...Interferon-inducible double-stranded RNA-dependent protein kinase activator A / PRKRA, first double-stranded RNA binding domain / PRKRA, second double-stranded RNA binding domain / PRKRA, third double-stranded RNA binding domain / Staufen, C-terminal / Staufen C-terminal domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Interferon-inducible double-stranded RNA-dependent protein kinase activator A homolog B
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SIR / Resolution: 1.9 Å
AuthorsRyter, J.M. / Schultz, S.C.
CitationJournal: EMBO J. / Year: 1998
Title: Molecular basis of double-stranded RNA-protein interactions: structure of a dsRNA-binding domain complexed with dsRNA.
Authors: Ryter, J.M. / Schultz, S.C.
History
DepositionNov 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 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
C: RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
D: RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
E: RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
G: RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
A: DOUBLE STRANDED RNA BINDING PROTEIN A
B: DOUBLE STRANDED RNA BINDING PROTEIN A


Theoretical massNumber of molelcules
Total (without water)28,2086
Polymers28,2086
Non-polymers00
Water6,467359
1
C: RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
D: RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
A: DOUBLE STRANDED RNA BINDING PROTEIN A
B: DOUBLE STRANDED RNA BINDING PROTEIN A


Theoretical massNumber of molelcules
Total (without water)21,7944
Polymers21,7944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')

E: RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,4142
Polymers6,4142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
3
G: RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')

G: RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,4142
Polymers6,4142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)110.400, 58.500, 58.900
Angle α, β, γ (deg.)90.00, 105.20, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

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


Mass: 3206.981 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: T7 TRANSCRIPTION OF SYNTHETIC DNA OLIGONUCLEOTIDES
#2: Protein DOUBLE STRANDED RNA BINDING PROTEIN A / XLRBPA


Mass: 7689.862 Da / Num. of mol.: 2 / Fragment: SECOND DSRNA BINDING DOMAIN / Mutation: N112M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91836
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: PEG 4000, ETHYLENE GLYCOL, KCL, NACL, MES, DTT, BETA-MERCAPTOETHANOL, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCL11
2NACL11
3MES11
4DTT11
5BETA-MERCAPTOETHANOL11
6ETHYLENE GLYCOL11
7PEG 400011
8ETHYLENE GLYCOL12
9PEG 400012
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.7 mMXlrbpa-21drop
20.7 mMr(GGCGCGCGCC)1drop
3225 mM1reservoirKCl
450 mM1reservoirNaCl
51 %PEG40001reservoir
612 %ehthylene glycol1reservoir
7100 mMMES1reservoir
810 mMdithiothreitol1reservoir
910 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 25, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→99 Å / Num. all: 28729 / Num. obs: 26083 / % possible obs: 90.8 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 10
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 1.66 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.5 / % possible all: 50
Reflection shell
*PLUS
% possible obs: 50 %

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIR / Resolution: 1.9→15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 346673.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3
Stereochemistry target values: ENGH & HUBER AND PARKINSON ET AL.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2406 9.9 %RANDOM
Rwork0.228 ---
all0.231 28633 --
obs0.231 24336 85.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.79 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1--7.03 Å20 Å2-1.99 Å2
2--10.7 Å20 Å2
3----3.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 848 0 373 2257
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d15.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.171.5
X-RAY DIFFRACTIONc_mcangle_it2.812
X-RAY DIFFRACTIONc_scbond_it2.852
X-RAY DIFFRACTIONc_scangle_it3.942.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 241 10 %
Rwork0.327 2177 -
obs--51 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PADNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAWATER.TOP
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg15.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.16

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