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- PDB-6rjf: Echovirus 1 intact particle -

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Basic information

Entry
Database: PDB / ID: 6rjf
TitleEchovirus 1 intact particle
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / VIRAL COAT PROTEIN / CAPSID / PICORNAVIRUS / ECHOVIRUS / ICOSAHEDRAL VIRUS
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / ec:3.4.22.29: / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / ec:3.4.22.28: / RNA-protein covalent cross-linking / T=pseudo3 icosahedral viral capsid ...caveolin-mediated endocytosis of virus by host cell / suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / ec:3.4.22.29: / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / ec:3.4.22.28: / RNA-protein covalent cross-linking / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / ec:3.6.1.15: / suppression by virus of host gene expression / ec:2.7.7.48: / induction by virus of host autophagy / ion channel activity / protein complex oligomerization / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-directed 5'-3' RNA polymerase activity / DNA replication / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding
Viral coat protein subunit / 3C cysteine protease (picornain 3C) / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA-directed RNA polymerase, C-terminal domain / Picornavirus coat protein VP4 superfamily / Picornavirus/Calicivirus coat protein / Picornavirus capsid / Picornavirus 2B protein / Picornavirus coat protein VP4 ...Viral coat protein subunit / 3C cysteine protease (picornain 3C) / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA-directed RNA polymerase, C-terminal domain / Picornavirus coat protein VP4 superfamily / Picornavirus/Calicivirus coat protein / Picornavirus capsid / Picornavirus 2B protein / Picornavirus coat protein VP4 / AAA+ ATPase domain / RNA-directed RNA polymerase, catalytic domain / picornavirus capsid protein / Peptidase S1, PA clan / Poliovirus core protein 3a, soluble domain / RNA dependent RNA polymerase / RNA helicase / Picornavirus core protein 2A / Picornavirus 2B protein / Picornavirus coat protein (VP4) / Poliovirus 3A protein like / RdRp of positive ssRNA viruses catalytic domain profile. / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded RNA virus / Picornavirales 3C/3C-like protease domain profile. / Poliovirus 3A protein-like / P-loop containing nucleoside triphosphate hydrolase / Peptidase C3, picornavirus core protein 2A
Genome polyprotein
Biological speciesEchovirus E1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDomanska, A. / Ruokolainen, V.P. / Pelliccia, M. / Laajala, M.A. / Marjomaki, V.S. / Butcher, S.J.
Funding supportFinland , 4件
OrganizationGrant numberCountry
Academy of Finland275199Finland
Academy of Finland315950Finland
Sigrid Juselius FoundationFinland
Jane and Aatos Erkko FoundationFinland
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 1996
Title: A pseudo-cell based approach to efficient crystallographic refinement of viruses.
Authors: D H Jacobson / J M Hogle / D J Filman /
Abstract: Strategies have been developed for the inexpensive refinement of atomic models of viruses and of other highly symmetric structures. These methods, which have been used in the refinement of several ...Strategies have been developed for the inexpensive refinement of atomic models of viruses and of other highly symmetric structures. These methods, which have been used in the refinement of several strains of poliovirus, focus on an arbitrary-sized parallelepiped (termed the 'protomer' box) containing a single complete averaged copy of the structural motif which forms the protein capsid, together with the fragments of other symmetry-related copies of the motif which are located in its immediate neighborhood. The Fourier transform of the protomer box provides reference structure factors for stereochemically restrained crystallographic refinement of the atomic model parameters. The phases of the reference structure factors are based on the averaged map, and are not permitted to change during the refinement. It is demonstrated that models refined using the protomer box methods do not differ significantly from models refined by more expensive full-cell calculations.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 26, 2019 / Release: Jun 12, 2019
RevisionDateData content typeProviderType
1.0Jun 12, 2019Structure modelrepositoryInitial release

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Structure viewerMolecule:
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Assembly

Deposited unit
1: VP1
2: VP2
3: VP3
4: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6025
Polymers94,3464
Non-polymers2561
Water0
1
1: VP1
2: VP2
3: VP3
4: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,676,136300
Polymers5,660,750240
Non-polymers15,38560
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area21690 Å2
ΔGint-107 kcal/mol
Surface area34740 Å2
MethodPISA

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Components

#1: Protein/peptide VP1


Mass: 31604.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E1 / Strain: Human/Egypt/Farouk/1951 / References: UniProt: O91734
#2: Protein/peptide VP2


Mass: 28872.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E1 / References: UniProt: O91734
#3: Protein/peptide VP3


Mass: 26471.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E1 / References: UniProt: O91734
#4: Protein/peptide VP4


Mass: 7398.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E1
#5: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Palmitic acid

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Echovirus E1 / Type: VIRUS / Entity ID: 1, 2, 3, 4 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Echovirus E1
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: icosahedralRegular icosahedron / Diameter: 300 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.2 / Details: 2 mM magnesium chloride in PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 979

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Processing

EM software
IDNameVersionCategoryFitting-ID
1RELION2.1particle selection
3EPUimage acquisition
5GctfCTF correction
8UCSF Chimeramodel fitting1
10Coot0.8.8model refinement1
14Coot0.8.9.1model refinement2
16MDFFmodel refinement3
17RELION2.1initial Euler assignment
19RELION2.1final Euler assignment
21RELION2.1classification
23RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 45309
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45309 / Symmetry type: POINT
Atomic model building
IDProtocolSpace
1RIGID BODY FIT
2FLEXIBLE FITREAL
3FLEXIBLE FITREAL
Atomic model building
IDPDB-ID3D fitting-ID
11EV11
21EV12
31EV13

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