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- PDB-3ks8: Crystal structure of Reston ebolavirus VP35 RNA binding domain in... -

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Basic information

Entry
Database: PDB / ID: 3ks8
TitleCrystal structure of Reston ebolavirus VP35 RNA binding domain in complex with 18bp dsRNA
Components
  • 5'-R(*AP*GP*AP*AP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*A)-3'
  • 5'-R(*UP*CP*CP*UP*CP*CP*CP*UP*CP*CP*CP*UP*CP*CP*UP*UP*CP*U)-3'
  • Polymerase cofactor VP35
KeywordsVIRAL PROTEIN/RNA / ebolavirus / RNA-binding protein / protein-RNA complex / interferon / Reston / Host cytoplasm / Interferon antiviral system evasion / RNA replication / RNA-binding / Transcription / Virion / VIRAL PROTEIN-RNA complex
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 / 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
RNA / RNA (> 10) / Polymerase cofactor VP35
Similarity search - Component
Biological speciesReston ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 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 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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
E: 5'-R(*AP*GP*AP*AP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*A)-3'
F: 5'-R(*UP*CP*CP*UP*CP*CP*CP*UP*CP*CP*CP*UP*CP*CP*UP*UP*CP*U)-3'
A: Polymerase cofactor VP35
B: Polymerase cofactor VP35
C: Polymerase cofactor VP35
D: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)93,7906
Polymers93,7906
Non-polymers00
Water2,702150
1
E: 5'-R(*AP*GP*AP*AP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*A)-3'
F: 5'-R(*UP*CP*CP*UP*CP*CP*CP*UP*CP*CP*CP*UP*CP*CP*UP*UP*CP*U)-3'
A: Polymerase cofactor VP35
B: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)52,6514
Polymers52,6514
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-R(*AP*GP*AP*AP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*A)-3'
F: 5'-R(*UP*CP*CP*UP*CP*CP*CP*UP*CP*CP*CP*UP*CP*CP*UP*UP*CP*U)-3'
C: Polymerase cofactor VP35
D: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)52,6514
Polymers52,6514
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.685, 85.685, 108.812
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: RNA chain 5'-R(*AP*GP*AP*AP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*A)-3'


Mass: 6056.748 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain 5'-R(*UP*CP*CP*UP*CP*CP*CP*UP*CP*CP*CP*UP*CP*CP*UP*UP*CP*U)-3'


Mass: 5455.203 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein
Polymerase cofactor VP35


Mass: 20569.424 Da / Num. of mol.: 4
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 365mM ammonium acetate, 100mM trisodium citrate, 18.5% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 12, 2009
RadiationMonochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.28→37.1 Å / Num. all: 40821 / Num. obs: 33227 / % possible obs: 81.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 23.47
Reflection shellResolution: 2.28→2.38 Å / Redundancy: 1.43 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 5.03 / Num. unique all: 1751 / % possible all: 35.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_222)refinement
HKL-2000data reduction
XPREPdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KS4

3ks4


Resolution: 2.401→35.117 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1499 5.05 %random
Rwork0.198 28170 --
obs0.2 29669 84.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.53 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso max: 128.04 Å2 / Biso mean: 42.743 Å2 / Biso min: 10.07 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.401→35.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3846 761 0 150 4757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0214834
X-RAY DIFFRACTIONf_angle_d1.3046679
X-RAY DIFFRACTIONf_dihedral_angle_d18.2291870
X-RAY DIFFRACTIONf_chiral_restr0.06774
X-RAY DIFFRACTIONf_plane_restr0.006730
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.4011-2.48690.3286550.24241101110133
2.4869-2.58640.3403900.27741658165851
2.5864-2.70410.34591280.27062507250775
2.7041-2.84660.33791730.26313058305893
2.8466-3.02490.29241790.252333103310100
3.0249-3.25830.30271760.220432773277100
3.2583-3.58590.25351900.199233143314100
3.5859-4.10410.21071860.171733173317100
4.1041-5.1680.17011760.155133013301100
5.168-35.12110.17461460.16813327332799

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