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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
Descriptorcapsid protein
KeywordsVIRAL PROTEIN / rubella virus capsid protein
Specimen sourceRubella virus / virus / RUBV / 風疹ウイルス
MethodElectron microscopy (35 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: 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: 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

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)
#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 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 deg. / Units: MEGADALTONS / Experimental flag: NO
Source (natural)Organism: Rubella virus strain M33
Source (recombinant)Organism: Escherichia coli BL21(DE3) / Plasmid: pTXB1 / Strain: Rosetta-2(DE3)
Buffer solutionpH: 7.2
Buffer component
IDConc.Conc. unitsNameFormulaBuffer ID
10.5Msodium chlorideNaCl1
20.05MTris-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 FIELD / 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
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1IMOD/PEET4.8.40/1.11.0VOLUME SELECTION1
2LeginonTomography 3.1IMAGE ACQUISITION1
4IMOD4.8.40CTF CORRECTION1
7EMfitMODEL FITTING1
13PEET1.11.0RECONSTRUCTION1
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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