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

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Basic information

Entry
Database: PDB / ID: 5khf
TitleFitted structure of rubella virus capsid protein
Componentscapsid proteinCapsid
KeywordsVIRAL PROTEIN / rubella virus capsid protein
Function / homologyRubella membrane glycoprotein E2 / Rubella capsid protein / Rubella capsid / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella membrane glycoprotein E1 / T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / clathrin-dependent endocytosis of virus by host cell ...Rubella membrane glycoprotein E2 / Rubella capsid protein / Rubella capsid / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella membrane glycoprotein E1 / T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral nucleocapsid / viral envelope / virion attachment to host cell / virion membrane / RNA binding / integral component of membrane / Structural polyprotein
Function and homology information
Specimen sourceRubella virus
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / 35 Å resolution
AuthorsMangala Prasad, V. / Klose, T. / Rossmann, M.G.
CitationJournal: PLoS Pathog. / Year: 2017
Title: Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus.
Authors: 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: 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 (Å2)5280
ΔGint (kcal/M)-41
Surface area (Å2)10410

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Components

#1: Protein/peptide capsid protein / Capsid


Mass: 30016.332 Da / Num. of mol.: 2 / Fragment: UNP residues 9-277 / Source: (gene. exp.) Rubella virus / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta-2 (DE3) / References: UniProt: P07566
#2: Water ChemComp-HOH / water


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

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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 strain M33 / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.064 MDa / Experimental value: NO
Source (natural)Organism: Rubella virus strain M33
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pTXB1 / Strain: Rosetta-2(DE3)
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer ID
10.5 Msodium chlorideNaCl1
20.05 MTris-ClC4H11NO31
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / 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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 11000 / Nominal defocus min: 500 nm
Image recordingElectron dose: 1 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1IMOD/PEET4.8.40/1.11.0volume selection
2LeginonTomography 3.1image acquisition
4IMOD4.8.40CTF correction
7EMfitmodel fitting
13PEET1.11.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 35 Å / Resolution method: OTHER / Number of particles: 18 / Symmetry type: POINT
EM volume selectionMethod: manual picking / Number of tomograms: 15 / Number of volumes extracted: 20 / Reference model: none
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: sumf

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