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- PDB-5khc: Structure of rubella virus E1 glycoprotein ectodomain fitted into... -

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Entry
Database: PDB / ID: 5khc
TitleStructure of rubella virus E1 glycoprotein ectodomain fitted into sub-tomogram averaged surface spike density of rubella virus
DescriptorE1 glycoprotein
KeywordsVIRAL PROTEIN / Rubella virus / surface glycoprotein spike / E1-E2 heterodimer
Specimen sourceRubella virus / virus / RUBV / 風疹ウイルス
MethodElectron microscopy (11.1 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: E1 glycoprotein


Theoretical massNumber of molelcules
Total (without water)50,5731
Polyers50,5731
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (A2)0
ΔGint (kcal/M)0
Surface area (A2)20940

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Components

#1: Polypeptide(L)E1 glycoprotein / p110


Mass: 50573.352 Da / Num. of mol.: 1 / Fragment: ectodomain (UNP residues 583-1018)
Source: (gene. exp.) Rubella virus / virus / 風疹ウイルス
References: UniProt: P08563

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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 E1-E2 glycoprotein spike / Type: COMPLEX
Specimen supportGrid material: COPPER / Grid mesh size: 200 /inch. / Grid type: Quantifoil R 1.2/1.3
VitrificationCryogen 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 max: 500 nm / Nominal defocus min: 400 nm

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Processing

3D reconstructionResolution: 11.1 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 7290
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: sumf
Atomic model buildingPDB-ID: 4ADG
Pdb chain id: A

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