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- PDB-4lg2: Crystal structure of Reston Ebola virus VP35 RNA binding domain b... -

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Basic information

Entry
Database: PDB / ID: 4lg2
TitleCrystal structure of Reston Ebola virus VP35 RNA binding domain bound to 12-bp dsRNA
Components
  • Polymerase cofactor
  • dsRNARNA
KeywordsRNA BINDING PROTEIN/RNA / RNA binding domain / dsRNA binding protein / dsRNA / RNA BINDING 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: 2.7 Å
AuthorsBale, S. / Julien, J.-P. / Bornholdt, Z.A. / Krois, A.S. / Wilson, I.A. / Saphire, E.O.
CitationJournal: J.Virol. / Year: 2013
Title: Ebolavirus VP35 coats the backbone of double-stranded RNA for interferon antagonism.
Authors: Bale, S. / Julien, J.P. / Bornholdt, Z.A. / Krois, A.S. / Wilson, I.A. / Saphire, E.O.
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Jun 14, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Sep 20, 2023Group: 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 / 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
B: Polymerase cofactor
C: Polymerase cofactor
D: Polymerase cofactor
E: dsRNA
F: dsRNA
J: dsRNA
I: dsRNA


Theoretical massNumber of molelcules
Total (without water)81,5068
Polymers81,5068
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.090, 72.871, 175.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Polymerase cofactor


Mass: 16564.113 Da / Num. of mol.: 4 / Fragment: UNP residues 205-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Reston ebolavirus / Strain: Reston / Gene: VP35, REBOVgp2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8JPY0
#2: RNA chain
dsRNA / RNA


Mass: 3812.320 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M Li2SO4, 0.1 M phosphate-citrate, pH 4.2 and 20% (w/v) PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2012
RadiationMonochromator: Asymmetric cut single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.7→39.3 Å / Num. all: 20077 / Num. obs: 20077 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.36 % / Biso Wilson estimate: 71 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.09 / Net I/σ(I): 8.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.49 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1968 / Rsym value: 0.574 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KS8

3ks8


Resolution: 2.7→39.296 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 30.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1016 5.07 %Random
Rwork0.2086 ---
obs0.2112 20027 99.46 %-
all-20077 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→39.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 887 0 8 4703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074884
X-RAY DIFFRACTIONf_angle_d1.0616807
X-RAY DIFFRACTIONf_dihedral_angle_d15.0931998
X-RAY DIFFRACTIONf_chiral_restr0.057800
X-RAY DIFFRACTIONf_plane_restr0.006730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7002-2.84250.3541410.27392665X-RAY DIFFRACTION100
2.8425-3.02050.36511520.26652670X-RAY DIFFRACTION100
3.0205-3.25360.32861440.24622691X-RAY DIFFRACTION100
3.2536-3.58090.30171510.23632658X-RAY DIFFRACTION100
3.5809-4.09850.28341410.19272720X-RAY DIFFRACTION100
4.0985-5.16190.18841580.18612727X-RAY DIFFRACTION99
5.1619-39.29970.25851290.1982880X-RAY DIFFRACTION99

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