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- PDB-6gbq: Crystal Structure of the oligomerization domain of Vp35 from Rest... -

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Basic information

Entry
Database: PDB / ID: 6gbq
TitleCrystal Structure of the oligomerization domain of Vp35 from Reston virus
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
Polymerase cofactor VP35
Similarity search - Component
Biological speciesReston ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.43 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
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Polymerase cofactor VP35
D: Polymerase cofactor VP35
E: Polymerase cofactor VP35
F: Polymerase cofactor VP35
G: Polymerase cofactor VP35
H: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)64,4028
Polymers64,4028
Non-polymers00
Water25214
1
A: Polymerase cofactor VP35
B: Polymerase cofactor VP35
C: Polymerase cofactor VP35
D: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)32,2014
Polymers32,2014
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12250 Å2
ΔGint-130 kcal/mol
Surface area14120 Å2
MethodPISA
2
E: Polymerase cofactor VP35
F: Polymerase cofactor VP35
G: Polymerase cofactor VP35
H: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)32,2014
Polymers32,2014
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
ΔGint-123 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.230, 45.583, 110.777
Angle α, β, γ (deg.)90.000, 101.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Polymerase cofactor VP35


Mass: 8050.256 Da / Num. of mol.: 8 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.74 Å3/Da / Density % sol: 55.17 % / Mosaicity: 0.1 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8 / Details: 20 % PEG-6000: 100 mM Na-acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.27982 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: 1.27982 Å / Relative weight: 1
ReflectionResolution: 2.43→47.52 Å / Num. obs: 26031 / % possible obs: 98.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.025 / Rrim(I) all: 0.064 / Net I/σ(I): 15.5 / Num. measured all: 172008
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.43-2.526.60.91727310.8160.3840.99699.4
9.09-47.525.60.0485140.9980.0210.05394.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.651
Highest resolutionLowest resolution
Rotation47.52 Å2.9 Å

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Processing

Software
NameVersionClassification
XDSNov 1, 2016data reduction
Aimless0.5.28data scaling
MOLREP11.4.06phasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GBR

6gbr


Resolution: 2.43→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 26.061 / SU ML: 0.265 / SU R Cruickshank DPI: 0.4146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.415 / ESU R Free: 0.292
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1246 4.8 %RANDOM
Rwork0.2468 ---
obs0.249 24764 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 154.52 Å2 / Biso mean: 77.104 Å2 / Biso min: 46.34 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å2-0 Å2-2.39 Å2
2--4.88 Å20 Å2
3----4.57 Å2
Refinement stepCycle: final / Resolution: 2.43→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3992 0 0 14 4006
Biso mean---58.84 -
Num. residues----530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194013
X-RAY DIFFRACTIONr_bond_other_d0.0010.023959
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.9885417
X-RAY DIFFRACTIONr_angle_other_deg0.88839097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8115522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92425.759158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12115772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9221523
X-RAY DIFFRACTIONr_chiral_restr0.0550.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024477
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02784
LS refinement shellResolution: 2.43→2.493 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 83 -
Rwork0.346 1813 -
all-1896 -
obs--99.32 %
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)
13.24570.90135.96931.1321.713211.9278-0.29060.04860.117-0.1249-0.1193-0.0049-0.37660.17230.40990.0604-0.00650.02510.12020.04240.181-21.71030.0269-2.2262
23.58322.58945.733.5635.774112.1033-0.2051-0.27870.3713-0.0097-0.38360.1805-0.2465-0.48110.58870.0851-0.0323-0.0190.10330.0490.1747-25.17612.60942.2893
30.48750.4281.35121.61292.92218.06570.0125-0.01550.02160.0077-0.0585-0.02970.0159-0.1140.0460.0021-0.0030.01680.10910.03560.2066-26.2906-0.73542.8251
41.213-0.03131.78411.40041.335512.3975-0.15390.17440.02990.0348-0.0871-0.04140.36090.90770.24090.05580.02330.0060.10230.070.2018-21.0233-2.55182.4198
50.616-1.30061.057411.1448-7.28715.8304-0.01930.17870.1476-0.3153-0.3172-0.48220.01590.20550.33660.21250.0995-0.04030.1931-0.06350.1304-3.3433-2.2529-26.0454
61.3149-2.41492.5796.4557-5.59066.9544-0.19070.28630.32680.2539-0.2476-0.4825-0.73420.23330.43820.23290.08680.01170.30420.04180.1886-4.64398.6171-29.9193
70.3181-0.29420.50713.897-5.50198.95790.028-0.00780.0325-0.04920.60550.4038-0.352-0.9213-0.63350.19230.0572-0.00250.1745-0.0080.1646-8.90763.3456-26.3377
80.30140.9605-1.04616.4186-7.35399.1050.04630.16110.2004-0.08350.23110.2478-0.2466-0.1552-0.27740.280.07460.04490.21350.06710.2366-8.60973.202-32.6169
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A72 - 141
2X-RAY DIFFRACTION2B72 - 136
3X-RAY DIFFRACTION3C72 - 140
4X-RAY DIFFRACTION4D71 - 138
5X-RAY DIFFRACTION5E71 - 132
6X-RAY DIFFRACTION6F75 - 141
7X-RAY DIFFRACTION7G71 - 136
8X-RAY DIFFRACTION8H76 - 138

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