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- PDB-3ajf: Structural insigths into dsRNA binding and RNA silencing suppress... -

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Basic information

Entry
Database: PDB / ID: 3ajf
TitleStructural insigths into dsRNA binding and RNA silencing suppression by NS3 protein of rice hoja blanca tenuivirus
ComponentsNon-structural protein 3
KeywordsVIRAL PROTEIN / RNA silencing suppression / negative strand RNA virus
Function / homology
Function and homology information


host cell cytoplasm / RNA binding
Similarity search - Function
Tenuivirus movement protein / Tenuivirus movement protein / Tenuivirus NS3 / Tenuivirus movement protein / de novo design (two linked rop proteins) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Suppressor of RNA silencing p3
Similarity search - Component
Biological speciesRice hoja blanca virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsYuan, Y.A.
CitationJournal: Rna / Year: 2011
Title: Structural implications into dsRNA binding and RNA silencing suppression by NS3 protein of Rice Hoja Blanca Tenuivirus
Authors: Yang, X. / Tan, S.H. / Teh, Y.J. / Yuan, Y.A.
History
DepositionJun 5, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 3
B: Non-structural protein 3
C: Non-structural protein 3
D: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,51112
Polymers44,7424
Non-polymers7698
Water2,432135
1
A: Non-structural protein 3
D: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7556
Polymers22,3712
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-18 kcal/mol
Surface area10510 Å2
MethodPISA
2
B: Non-structural protein 3
C: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7556
Polymers22,3712
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-18 kcal/mol
Surface area10570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.690, 79.690, 122.087
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11D-126-

HOH

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Components

#1: Protein
Non-structural protein 3


Mass: 11185.555 Da / Num. of mol.: 4 / Fragment: helix domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rice hoja blanca virus / Strain: cr / Gene: NS3 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q67897
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sulfate, MPD, cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2009
RadiationMonochromator: 180 degree / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 25361 / Num. obs: 25361 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.109
Reflection shellResolution: 2→2.03 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.429 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→34.21 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.052 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25474 1349 5.1 %RANDOM
Rwork0.21232 ---
all0.214 25361 --
obs0.2144 25361 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.881 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2---0.56 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 2→34.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 40 135 3173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223122
X-RAY DIFFRACTIONr_angle_refined_deg1.5342.0054248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4625359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32123.529136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02415547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5121516
X-RAY DIFFRACTIONr_chiral_restr0.10.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022300
X-RAY DIFFRACTIONr_nbd_refined0.2150.21371
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22129
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2125
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.222
X-RAY DIFFRACTIONr_mcbond_it1.3421.51917
X-RAY DIFFRACTIONr_mcangle_it1.67523018
X-RAY DIFFRACTIONr_scbond_it3.3831378
X-RAY DIFFRACTIONr_scangle_it4.4664.51230
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 95 -
Rwork0.21 1792 -
obs--96.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.89380.4301-0.1631.9897-0.66141.54010.0143-0.103-0.05290.12530.0642-0.0240.0254-0.0365-0.0785-0.05030.01170.0135-0.04140.0118-0.050626.853616.284744.7118
21.85540.3250.52021.060.06741.39790.03330.1420.0093-0.07440.02350.06530.0509-0.0288-0.0568-0.04180.0115-0.0193-0.0324-0.0222-0.064716.280626.849715.4251
31.5322-0.5164-0.50231.33620.55251.70020.01580.02250.1836-0.06280.0568-0.1196-0.0625-0.0948-0.0726-0.04120.0040.0135-0.0708-0.0204-0.043716.937539.598430.0922
41.5488-0.0085-0.53071.5530.42242.22750.0162-0.10160.08990.03010.0153-0.18140.10160.0874-0.0315-0.06830.011-0.004-0.0355-0.0164-0.041639.602216.871430.1551
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 113
2X-RAY DIFFRACTION2B22 - 113
3X-RAY DIFFRACTION3C25 - 113
4X-RAY DIFFRACTION4D24 - 113

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