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- PDB-5khe: Fitted structure of rubella virus capsid protein -

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Entry
Database: PDB / ID: 5khe
TitleFitted structure of rubella virus capsid protein
Descriptorcapsid protein
KeywordsVIRAL PROTEIN / rubella virus capsid protein
Specimen sourceRubella virus / virus / RUBV / 風疹ウイルス
MethodElectron microscopy (35 A resolution / Subtomogram averaging)
AuthorsMangala Prasad, V. / Klose, T. / Rossmann, M.G.
CitationPlos Pathog., 2017

Plos Pathog., 2017
Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus
Mangala Prasad, V. / Klose, T. / Rossmann, M.G.

DateDeposition: Jun 14, 2016 / Release: May 10, 2017

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Assembly

Deposited unit
A: capsid protein
B: capsid protein


Theoretical massNumber of molelcules
Total (without water)60,0332
Polyers60,0332
Non-polymers00
Water63135
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (A2)5290
ΔGint (kcal/M)-41
Surface area (A2)10400

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Components

#1: Polypeptide(L)capsid protein


Mass: 30016.332 Da / Num. of mol.: 2 / Fragment: UNP residues 9-277
Source: (gene. exp.) Rubella virus / virus / 風疹ウイルス
References: UniProt: P07566
#2: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SUBTOMOGRAM AVERAGING

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Sample preparation

ComponentName: Rubella virus strain M33 / Type: COMPLEX
Specimen supportGrid material: COPPER / Grid mesh size: 200 /inch. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 11000 X / Nominal defocus min: 500 nm

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Processing

3D reconstructionResolution: 35 A / Resolution method: OTHER / Number of particles: 18
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: sumf

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