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- PDB-6gbp: Crystal Structure of the oligomerization domain of VP35 from Ebol... -

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Basic information

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


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 cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / symbiont-mediated suppression of host PKR/eIFalpha signaling / positive regulation of protein sumoylation / viral transcription / molecular sequestering activity ...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 cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / symbiont-mediated suppression of host PKR/eIFalpha signaling / positive regulation of protein sumoylation / viral transcription / molecular sequestering activity / viral genome replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral nucleocapsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.49 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 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,43923
Polymers99,23312
Non-polymers2,20611
Water00
1
A: Polymerase cofactor VP35
B: Polymerase cofactor VP35
C: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6117
Polymers24,8083
Non-polymers8024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-108 kcal/mol
Surface area15490 Å2
MethodPISA
2
D: Polymerase cofactor VP35
E: Polymerase cofactor VP35
F: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0094
Polymers24,8083
Non-polymers2011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-83 kcal/mol
Surface area15620 Å2
MethodPISA
3
G: Polymerase cofactor VP35
H: Polymerase cofactor VP35
I: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2095
Polymers24,8083
Non-polymers4012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-91 kcal/mol
Surface area15620 Å2
MethodPISA
4
J: Polymerase cofactor VP35
K: Polymerase cofactor VP35
L: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6117
Polymers24,8083
Non-polymers8024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-105 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.421, 103.923, 186.287
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.) Zaire ebolavirus / Gene: VP35 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05127
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Hg

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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: 3 Å3/Da / Density % sol: 58.94 % / Mosaicity: 0.25 °
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 7.5 / Details: 50 mM HEPES-NaOH pH 7.5, 2.6 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: 3.49→46.57 Å / Num. obs: 15726 / % possible obs: 99.2 % / Redundancy: 16.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.242 / Rpim(I) all: 0.06 / Rrim(I) all: 0.249 / Net I/σ(I): 10 / Num. measured all: 262316 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.49-3.8216.91.1896083535950.8020.2941.2262.996.8
8.55-46.5714.20.0671686811870.9990.0170.06933.199.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
REFMACrefinement
XDSVERSION Oct 15, 2015data reduction
Aimless0.3.11data scaling
SHELXDE2013/2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 3.49→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.2611 / WRfactor Rwork: 0.1987 / FOM work R set: 0.7975 / SU B: 34.358 / SU ML: 0.511 / SU Rfree: 0.6856 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.686 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2811 739 4.9 %RANDOM
Rwork0.2208 ---
obs0.2237 14401 95.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 238.74 Å2 / Biso mean: 99.538 Å2 / Biso min: 57.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å20 Å2
2--0.15 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3.49→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6594 0 11 0 6605
Biso mean--143.27 --
Num. residues----849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196679
X-RAY DIFFRACTIONr_bond_other_d0.0010.026423
X-RAY DIFFRACTIONr_angle_refined_deg0.9861.9539059
X-RAY DIFFRACTIONr_angle_other_deg0.853314753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4945835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67225.627295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.987151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7741521
X-RAY DIFFRACTIONr_chiral_restr0.0450.21121
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021435
LS refinement shellResolution: 3.491→3.581 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 38 -
Rwork0.313 902 -
all-940 -
obs--82.02 %

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