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- PDB-5nd1: Viral evolution results in multiple, surface-allocated enzymatic ... -

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Entry
Database: PDB / ID: 5nd1
TitleViral evolution results in multiple, surface-allocated enzymatic activities in a fungal double-stranded RNA virus
DescriptorCapsid protein
KeywordsVIRUS / RnQV1 / dsRNA virus / fungal virus / virus
Specimen sourceRosellinia necatrix quadrivirus 1 / virus / RnQV1
MethodElectron microscopy (3.7 Å resolution / Particle / Single particle)
AuthorsMata, C.P. / Luque, D. / Gomez Blanco, J. / Rodriguez, J.M. / Suzuki, N. / Ghabrial, S.A. / Carrascosa, J.L. / Trus, B.L. / Caston, J.R.
CitationTo Be Published

To Be Published Search PubMed
Viral evolution results in multiple, surface-allocated enzymatic activities in a fungal double-stranded RNA virus
Mata, C.P. / Luque, D. / Gomez-Blanco, J. / Rodriguez, J.M. / Suzuki, N. / Ghabrial, S.A. / Carrascosa, J.L. / Trus, B.L. / Caston, J.R.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 7, 2017 / Release: Nov 29, 2017

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)261,2222
Polyers261,2222
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)15600
ΔGint (kcal/M)-85
Surface area (Å2)68510
MethodPISA

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Components

#1: Polypeptide(L)Capsid protein


Mass: 147782.375 Da / Num. of mol.: 1 / Source: (natural) Rosellinia necatrix quadrivirus 1 / virus / References: UniProt: M1VMJ0
#2: Polypeptide(L)Capsid protein


Mass: 113439.344 Da / Num. of mol.: 1 / Source: (natural) Rosellinia necatrix quadrivirus 1 / virus / References: UniProt: M1VHN2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: virus / Type: VIRUS / Entity ID: 1, 2
Molecular weightValue: 15.9 deg. / Units: MEGADALTONS / Experimental value: YES
Details of virusEmpty: YES / Enveloped: NO / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Rosellinia necatrix
Virus shellName: P2 and P4 capsid proteins / Diameter: 470 Å / Triangulation number (T number): 1
Buffer solutionDetails: 50 mM Tris-HCl pH 7.8, 150 mM NaCl, 5 mM EDTA / pH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 300 / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM CPC / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated defocus min: 700 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 1.7 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 24 / Used frames/image: 4-21

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Processing

EM software
IDNameVersionCategoryImage processing IDFitting ID
1Xmipp3PARTICLE SELECTION1
4CTFFIND3CTF CORRECTION1
7CootMODEL FITTING1
9RELION1.4INITIAL EULER ASSIGNMENT1
10RELION1.4FINAL EULER ASSIGNMENT1
11RELION1.4CLASSIFICATION1
12RELION1.4RECONSTRUCTION1
13CootMODEL REFINEMENT1
14REFMAC5MODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNumber of particles selected: 53683
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 37531 / Symmetry type: POINT
Atomic model buildingRef protocol: BACKBONE TRACE

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