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- PDB-3ks4: Crystal structure of Reston ebolavirus VP35 RNA binding domain -

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Basic information

Entry
Database: PDB / ID: 3ks4
TitleCrystal structure of Reston ebolavirus VP35 RNA binding domain
ComponentsPolymerase cofactor VP35
KeywordsVIRAL PROTEIN / RNA BINDING PROTEIN / ebolavirus / RNA-binding protein / protein-RNA complex / interferon / Reston / Host cytoplasm / Interferon antiviral system evasion / RNA replication / RNA-binding / Transcription / Virion
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / virion component / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / virus-mediated perturbation of host defense response / RNA binding
Similarity search - Function
Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain / Filoviridae VP35, C-terminal inhibitory domain, helical subdomain / Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / Seminal Fluid Protein PDC-109 (Domain B) / Helicase, Ruva Protein; domain 3 ...Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain / Filoviridae VP35, C-terminal inhibitory domain, helical subdomain / Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / Seminal Fluid Protein PDC-109 (Domain B) / Helicase, Ruva Protein; domain 3 / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Polymerase cofactor VP35
Similarity search - Component
Biological speciesReston ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKimberlin, C.R. / Bornholdt, Z.A. / Li, S. / Woods, V.L. / Macrae, I.J. / Saphire, E.O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Ebolavirus VP35 uses a bimodal strategy to bind dsRNA for innate immune suppression.
Authors: Kimberlin, C.R. / Bornholdt, Z.A. / Li, S. / Woods, V.L. / Macrae, I.J. / Saphire, E.O.
History
DepositionNov 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase cofactor VP35
B: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)41,1392
Polymers41,1392
Non-polymers00
Water1,47782
1
A: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)20,5691
Polymers20,5691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)20,5691
Polymers20,5691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.160, 158.160, 166.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Polymerase cofactor VP35


Mass: 20569.424 Da / Num. of mol.: 2
Fragment: C-terminal RNA binding domain (UNP residues 160-329)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Reston ebolavirus / Strain: Reston / Gene: REBOVgp2, VP35 / Plasmid: pET46 EK/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8JPY0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 4.86 Å3/Da / Density % sol: 74.69 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 90mM tripostassium citrate, 100mM sodium acetate, 5% (wt/vol) PEG 6000, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2008
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→45.66 Å / Num. all: 30140 / Num. obs: 30094 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.71 % / Biso Wilson estimate: 55.46 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.65 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2 / Num. unique all: 3050 / % possible all: 97.9

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Processing

Software
NameVersionClassification
EPICS-basedbeamline controldata collection
dataacquisition systemsdata collection
SHARPphasing
PHENIX(phenix.refine: 1.4_151)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→45.657 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1517 5.04 %random
Rwork0.198 28577 --
obs0.199 30094 95.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.413 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 165.04 Å2 / Biso mean: 64.169 Å2 / Biso min: 24.79 Å2
Baniso -1Baniso -2Baniso -3
1--6.508 Å2-0 Å20 Å2
2---6.508 Å20 Å2
3---13.015 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 0 82 2031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081997
X-RAY DIFFRACTIONf_angle_d1.022704
X-RAY DIFFRACTIONf_dihedral_angle_d16.884769
X-RAY DIFFRACTIONf_chiral_restr0.065301
X-RAY DIFFRACTIONf_plane_restr0.006350
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3999-2.48570.33451690.30452872287298
2.4857-2.58520.3591600.28762856285697
2.5852-2.70290.31861410.25552860286097
2.7029-2.84530.27481530.2422869286997
2.8453-3.02360.24491550.21992867286797
3.0236-3.2570.23921570.21612857285796
3.257-3.58460.23231450.19412873287396
3.5846-4.1030.18051330.16352862286295
4.103-5.16830.15131560.13572827282795
5.1683-45.66510.15871480.14482834283492
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)
11.13070.53810.74451.08250.88573.37860.02210.0145-0.1119-0.1397-0.1771-0.2671-0.90220.34110.26670.4092-0.084-0.10690.39450.02120.6065-1.3829.364975.2863
28.71142.80561.69691.6478-1.2634.7297-0.42640.20031.8195-0.5151-0.22360.5788-0.7585-0.02410.52190.4942-0.0513-0.07570.37870.12960.516-1.994925.955864.2493
33.0206-0.6608-0.53181.63161.07370.7035-0.2242-0.02040.28270.1194-0.13750.5271-0.0094-0.03180.22520.3302-0.0081-0.11340.31770.03810.3149-9.305121.225168.3588
42.0239-0.0996-0.2572.1529-0.97180.4817-0.09680.20930.2907-0.429-0.0817-0.4673-0.0570.33780.19460.4088-0.0287-0.04220.31990.04280.38212.498117.576469.8549
52.60680.6103-1.46360.9151-0.00282.1347-0.2732-0.28180.12580.069-0.14410.2586-0.1584-0.06280.35240.2865-0.0109-0.09580.2721-0.06740.3343-12.662414.567572.2767
62.27031.28460.60793.9454-2.76393.3128-0.76880.75990.2836-1.49360.26030.70710.5622-0.2660.23460.4879-0.0302-0.25440.6518-0.02050.4623-19.533716.122259.179
72.9839-1.331.03761.49880.13482.1211-0.5980.54830.44670.04960.4089-0.64180.10510.50280.09140.30710.0175-0.10990.4606-0.08830.3974-15.62198.004670.9723
83.7546-0.7077-0.44283.30210.22112.7657-0.25691.5310.7212-0.2881-0.54980.8524-0.209-0.59290.70020.39810.0352-0.17170.5142-0.13120.7226-24.651514.970166.8538
91.2016-0.02570.52531.2312-0.10550.23630.2323-0.453-0.3241-0.1570.20980.53720.6117-0.59-0.47450.6189-0.075-0.15870.41180.16520.43736.989529.771956.0544
102.00710.11230.32660.39680.38720.58550.05340.20520.313-0.0192-0.2739-0.2461-0.2595-0.04850.20540.5703-0.059-0.05740.39850.17130.539811.464333.909962.8652
110.0795-0.4749-0.01992.8050.1080.1827-0.0071-0.17610.13280.03040.2248-1.54460.56310.04210.23310.484-0.00730.07080.37620.2270.6120.354324.859262.3008
123.1863-2.1613-0.61521.57730.47260.21810.22781.2072-0.0891-0.3383-0.8647-1.61880.24360.18750.65360.5035-0.0621-0.04330.43840.27660.855122.795933.519963.0663
133.2411-1.2537-0.28941.82781.09121.65640.2525-0.23280.85520.4047-0.1389-0.1119-0.0309-0.2771-0.04270.7134-0.07490.01520.40890.16670.654610.868943.85371.5975
140.3959-0.5408-0.10630.94960.18210.55220.3127-0.31960.27340.90930.0441-1.2719-1.11751.4405-0.13321.0459-0.3101-0.13340.78170.01910.881619.235246.045275.6468
155.5805-0.93670.48495.38090.9856.65210.36080.50071.2883-0.0409-0.3196-1.08450.21990.62270.17880.5669-0.1048-0.12610.44890.13340.810222.558343.180668.8875
160.4253-0.2333-0.56070.59930.73691.85650.44520.03620.1452-0.2244-0.78590.6413-1.0516-0.47220.020.8487-0.0734-0.01160.3993-0.01040.759611.36347.752575.6871
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 205:214)A205 - 214
2X-RAY DIFFRACTION2(chain A and resid 215:220)A215 - 220
3X-RAY DIFFRACTION3(chain A and resid 221:242)A221 - 242
4X-RAY DIFFRACTION4(chain A and resid 243:266)A243 - 266
5X-RAY DIFFRACTION5(chain A and resid 267:290)A267 - 290
6X-RAY DIFFRACTION6(chain A and resid 291:302)A291 - 302
7X-RAY DIFFRACTION7(chain A and resid 303:316)A303 - 316
8X-RAY DIFFRACTION8(chain A and resid 317:329)A317 - 329
9X-RAY DIFFRACTION9(chain B and resid 206:216)B206 - 216
10X-RAY DIFFRACTION10(chain B and resid 217:249)B217 - 249
11X-RAY DIFFRACTION11(chain B and resid 250:263)B250 - 263
12X-RAY DIFFRACTION12(chain B and resid 264:273)B264 - 273
13X-RAY DIFFRACTION13(chain B and resid 274:297)B274 - 297
14X-RAY DIFFRACTION14(chain B and resid 298:308)B298 - 308
15X-RAY DIFFRACTION15(chain B and resid 309:313)B309 - 313
16X-RAY DIFFRACTION16(chain B and resid 314:329)B314 - 329

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