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- PDB-6gbr: Crystal Structure of the oligomerization domain of VP35 from Rest... -

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Basic information

Entry
Database: PDB / ID: 6gbr
TitleCrystal Structure of the oligomerization domain of VP35 from Reston virus, mercury derivative
ComponentsPolymerase cofactor VP35
KeywordsVIRAL PROTEIN / coiled-coil
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
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.
Similarity search - Domain/homology
MERCURIBENZOIC ACID / Polymerase cofactor VP35
Similarity search - Component
Biological speciesReston ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.15 Å
AuthorsZinzula, L. / Nagy, I. / Orsini, M. / Weyher-Stingl, E. / Baumeister, W. / Bracher, A.
CitationJournal: Structure / Year: 2019
Title: Structures of Ebola and Reston Virus VP35 Oligomerization Domains and Comparative Biophysical Characterization in All Ebolavirus Species.
Authors: Zinzula, L. / Nagy, I. / Orsini, M. / Weyher-Stingl, E. / Bracher, A. / Baumeister, W.
History
DepositionApr 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase cofactor VP35
B: Polymerase cofactor VP35
C: Polymerase cofactor VP35
D: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8446
Polymers32,2014
Non-polymers6432
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12310 Å2
ΔGint-138 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.933, 91.901, 104.193
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Polymerase cofactor VP35


Mass: 8050.256 Da / Num. of mol.: 4 / Fragment: oligomerization domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Reston ebolavirus / Gene: VP35, REBOVgp2 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8JPY0
#2: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5HgO2

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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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: 25 % PEG-6000, 100 mM MES-Na, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.00904 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00904 Å / Relative weight: 1
ReflectionResolution: 3.14→45.95 Å / Num. obs: 6505 / % possible obs: 99.5 % / Redundancy: 47 % / Biso Wilson estimate: 93.12 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.022 / Rrim(I) all: 0.149 / Net I/σ(I): 21.4 / Num. measured all: 305959 / Scaling rejects: 45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.14-3.3537.61.11111320.8160.1811.12897.5
8.87-45.9538.50.07234010.0110.07399.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSVERSION Nov 1, 2016data reduction
Aimless0.5.28data scaling
SHELXDE2013/2phasing
PHENIX1.8.2refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 3.15→29.579 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.86
RfactorNum. reflection% reflection
Rfree0.3113 352 5.51 %
Rwork0.207 --
obs0.2125 6383 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 348.21 Å2 / Biso mean: 92.76 Å2 / Biso min: 35.92 Å2
Refinement stepCycle: final / Resolution: 3.15→29.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 28 0 2123
Biso mean--120.49 --
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0232136
X-RAY DIFFRACTIONf_angle_d1.8962875
X-RAY DIFFRACTIONf_chiral_restr0.077350
X-RAY DIFFRACTIONf_plane_restr0.007364
X-RAY DIFFRACTIONf_dihedral_angle_d17.05816
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1501-3.60530.4131140.270619692083
3.6053-4.53960.34351210.202119742095
4.5396-29.58070.2631170.192120882205
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)
11.0559-0.10160.28351.5427-0.27560.5125-0.6686-0.0958-1.30960.0153-0.08060.28980.3713-0.2018-0.21180.2442-0.0423-0.2180.38050.02280.477144.652777.1441-1.7512
20.8434-0.1705-0.72770.87780.00320.020.30040.47-0.539-0.1881-0.4730.2065-0.5577-0.40950.00350.44030.1107-0.01930.5176-0.11870.406143.493782.8503-4.0687
30.6705-0.46040.20860.2968-0.06560.20920.2639-0.205-0.16480.1042-0.14310.0686-0.4224-0.15950.65230.7424-0.02830.04080.55-0.08450.389643.967784.64090.7479
42.00720.1453-1.96520.6068-0.27631.31850.2045-0.6963-0.61710.0889-0.5213-0.0389-0.59880.7084-0.21120.4558-0.12150.00390.63390.01840.455648.424578.9574-0.4358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 72 through 138 )A72 - 138
2X-RAY DIFFRACTION2chain 'B' and (resid 72 through 137 )B72 - 137
3X-RAY DIFFRACTION3chain 'C' and (resid 72 through 141 )C72 - 141
4X-RAY DIFFRACTION4chain 'D' and (resid 71 through 137 )D71 - 137

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