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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 Å resolution / Particle / Subtomogram averaging)
AuthorsMangala Prasad, V. / Klose, T. / Rossmann, M.G.
CitationPLoS Pathog., 2017, 13, e1006377-e1006377

PLoS Pathog., 2017, 13, e1006377-e1006377 StrPapers
Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus.
Vidya Mangala Prasad / Thomas Klose / Michael G Rossmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 14, 2016 / Release: May 10, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 10, 2017Structure modelrepositoryInitial release
1.1Jun 14, 2017Structure modelDatabase referencescitation_citation.country / _citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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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 (Å2)0
ΔGint (kcal/M)0
Surface area (Å2)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

Cellular component

Molecular function

Biological process

  • clathrin-dependent endocytosis of virus by host cell (GO: 0075512)
  • fusion of virus membrane with host endosome membrane (GO: 0039654)
  • virion attachment to host cell (GO: 0019062)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SUBTOMOGRAM AVERAGING

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Sample preparation

ComponentName: Rubella virus E1-E2 glycoprotein spike / Type: COMPLEX / Entity ID: 1 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.085 deg. / Units: MEGADALTONS / Experimental flag: NO
Buffer solutionpH: 8
Buffer component
IDConc.Conc. unitsNameFormulaBuffer ID
10.02MTrisC4H11NO31
20.12Msodium chlorideNaCl1
30.001MEDTAC10H16N2O81
SpecimenConc.: 1 mg/ml
Details: Rubella virus was purified from Vero cells. Glycoprotein spike volumes were extracted from the surface of virus tomograms.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R 1.2/1.3
VitrificationCryogen 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 11000 / Nominal defocus max: 500 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 90 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1IMOD/PEET4.8.40/1.11.0VOLUME SELECTION1
2LeginonTomgraphy 3.1IMAGE ACQUISITION1
4IMOD4.8.40CTF CORRECTION1
7EMfitMODEL FITTING1
11PEET1.11.0FINAL EULER ASSIGNMENT1
12PEET1.11.0CLASSIFICATION1
13PEET1.11.0RECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 11.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 7290 / Symmetry type: POINT
EM volume selectionMethod: manual picking / Number of tomograms: 15 / Number of volumes extracted: 7500
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: sumf
Atomic model buildingPDB-ID: 4ADG
Pdb chain ID: A / Pdb chain residue range: 1-421

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