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- PDB-6gbo: Crystal Structure of the oligomerization domain of Vp35 from Ebol... -

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Basic information

Entry
Database: PDB / ID: 6gbo
TitleCrystal Structure of the oligomerization domain of Vp35 from Ebola virus
ComponentsPolymerase cofactor VP35
KeywordsVIRAL PROTEIN / coiled-coil
Function / homology
Function and homology information


suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host innate immune response / 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 / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / positive regulation of protein sumoylation ...suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host innate immune response / 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 / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / positive regulation of protein sumoylation / molecular sequestering activity / viral transcription / viral genome replication / 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 / viral nucleocapsid / host cell cytoplasm / negative regulation of gene expression / 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 speciesEbola virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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
I: Polymerase cofactor VP35
J: Polymerase cofactor VP35
K: Polymerase cofactor VP35
L: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)99,23312
Polymers99,23312
Non-polymers00
Water3,117173
1
A: Polymerase cofactor VP35
B: Polymerase cofactor VP35
C: Polymerase cofactor VP35
D: Polymerase cofactor VP35
E: Polymerase cofactor VP35
F: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)49,6166
Polymers49,6166
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19730 Å2
ΔGint-207 kcal/mol
Surface area21450 Å2
MethodPISA
2
G: Polymerase cofactor VP35
H: Polymerase cofactor VP35
I: Polymerase cofactor VP35
J: Polymerase cofactor VP35
K: Polymerase cofactor VP35
L: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)49,6166
Polymers49,6166
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19240 Å2
ΔGint-201 kcal/mol
Surface area21590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.782, 98.907, 185.069
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: 8269.400 Da / Num. of mol.: 12 / Fragment: oligomerization domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus / Gene: VP35 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05127
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.94 Å3/Da / Density % sol: 58.18 % / Mosaicity: 0.08 °
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 7.5 / Details: 50 mM HEPES-NaOH pH 7.5, 2.5 M Na-acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.008 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.1→49.45 Å / Num. obs: 69399 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.031 / Rrim(I) all: 0.112 / Net I/σ(I): 16 / Num. measured all: 902583
Reflection shell

Diffraction-ID: 1 / % possible all: 98.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
2.1-2.1512.41.63343580.5580.4771.703
10.06-49.4510.90.0327350.9990.010.034

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.573
Highest resolutionLowest resolution
Rotation47.78 Å3 Å

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Processing

Software
NameVersionClassification
XDSVERSION Oct 15, 2015data reduction
Aimless0.1.27data scaling
MOLREP11.2.08phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GBP

6gbp


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.357 / SU ML: 0.132 / SU R Cruickshank DPI: 0.1899 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.167
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 3501 5.1 %RANDOM
Rwork0.2107 ---
obs0.2123 65799 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 150 Å2 / Biso mean: 56.177 Å2 / Biso min: 25.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å2-0 Å20 Å2
2---0.55 Å2-0 Å2
3----1.24 Å2
Refinement stepCycle: final / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6669 0 0 173 6842
Biso mean---46 -
Num. residues----852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196758
X-RAY DIFFRACTIONr_bond_other_d0.0010.026555
X-RAY DIFFRACTIONr_angle_refined_deg1.0771.9549158
X-RAY DIFFRACTIONr_angle_other_deg0.737315072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2435840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14425.418299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.386151241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1191524
X-RAY DIFFRACTIONr_chiral_restr0.0580.21128
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027546
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021456
LS refinement shellResolution: 2.098→2.152 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 276 -
Rwork0.294 4713 -
all-4989 -
obs--98.75 %
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)
11.1389-1.0572-2.12392.26142.95255.3549-0.1420.2056-0.14190.0446-0.16470.18470.5408-0.09270.30670.23840.06560.0070.2350.00340.245551.201116.1283-21.0985
20.7878-0.7163-0.74374.40353.99015.2593-0.01350.1979-0.1162-0.2848-0.0328-0.05430.23120.03550.04640.21320.04210.06550.1958-0.01360.289854.205916.3054-22.378
30.4779-0.0034-0.12112.84834.70459.8703-0.0010.1513-0.0336-0.37250.0607-0.0821-0.35510.0989-0.05970.20310.08120.01320.226-0.01380.317658.679115.581-25.0807
41.18641.95691.42069.70075.9134.8855-0.0072-0.07570.11510.2181-0.25530.40860.0613-0.2130.26250.0284-0.00050.0630.12480.01080.201238.542349.81277.3449
51.6448-2.4013-1.6366.14393.80054.0723-0.0951-0.16820.13950.47650.15580.00760.15190.1357-0.06070.077-0.05110.02250.1409-0.00990.240843.90444.16959.5273
60.95590.07610.10765.25634.82696.6482-0.0079-0.07470.02240.3041-0.07610.0978-0.0114-0.13720.0840.06510.01790.04470.07970.04530.20442.336546.64598.3988
71.44451.24632.21673.00932.92396.2063-0.0678-0.24750.14350.2294-0.08750.0507-0.31240.12450.15520.1141-0.0290.03280.18680.00250.203758.563480.082719.3925
80.88330.39580.42825.48355.24097.27740.0151-0.2080.04290.36480.161-0.2182-0.13940.2871-0.17610.131-0.0283-0.03760.14630.05450.218460.239878.534922.373
90.7809-0.7049-1.45073.98745.802310.56790.0238-0.1740.03930.5030.1507-0.16970.29470.2008-0.17450.184-0.0133-0.02270.18750.03570.261764.093677.400826.58
100.76120.01350.01098.39494.76783.72060.0450.101-0.0773-0.3419-0.17390.1083-0.0168-0.19990.12890.05130.0043-0.01420.15360.0180.151543.021953.1518-12.4016
111.97752.51.97865.17444.06444.6584-0.11420.2059-0.162-0.36630.1759-0.03940.01380.103-0.06170.10090.0170.00450.11480.03340.226750.594155.5098-11.5884
120.97790.21170.18175.77164.91266.0411-0.09650.2076-0.0865-0.41220.07680.0196-0.06110.02450.01970.0857-0.04410.00380.10610.02980.176647.602254.0694-11.3779
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A81 - 153
2X-RAY DIFFRACTION2B81 - 153
3X-RAY DIFFRACTION3C81 - 147
4X-RAY DIFFRACTION4D81 - 149
5X-RAY DIFFRACTION5E81 - 153
6X-RAY DIFFRACTION6F81 - 153
7X-RAY DIFFRACTION7G82 - 153
8X-RAY DIFFRACTION8H82 - 153
9X-RAY DIFFRACTION9I82 - 147
10X-RAY DIFFRACTION10J81 - 150
11X-RAY DIFFRACTION11K82 - 153
12X-RAY DIFFRACTION12L82 - 153

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