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- PDB-6iln: Cryo-EM structure of full Echovirus 6 particle at PH 5.5 -

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Entry
Database: PDB / ID: 6iln
TitleCryo-EM structure of full Echovirus 6 particle at PH 5.5
Components
  • Capsid protein VP1
  • Capsid protein VP2
  • Capsid protein VP3
  • Capsid protein VP4
KeywordsVIRUS
Specimen sourceEchovirus E6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGao, G.F. / Liu, S. / Zhao, X. / Peng, R.
Funding supportChina , 1件
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010000China
CitationJournal: To Be Published
Title: structure of full Echovirus 6 particle
Authors: Liu, S. / Peng, R. / Zhao, X. / George, F.G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 19, 2018 / Release: May 15, 2019Array

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-9688
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-9688
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3335
Polymers93,0334
Non-polymers2991
Water0
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,599,967300
Polymers5,581,998240
Non-polymers17,97060
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area21020 Å2
ΔGint-104 kcal/mol
Surface area34750 Å2
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 467 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)466,66425
Polymers465,16620
Non-polymers1,4975
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 560 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)559,99730
Polymers558,20024
Non-polymers1,7976
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein/peptide Capsid protein VP1 /


Mass: 31364.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E6
#2: Protein/peptide Capsid protein VP2 /


Mass: 28064.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E6
#3: Protein/peptide Capsid protein VP3 /


Mass: 26378.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E6
#4: Protein/peptide Capsid protein VP4 /


Mass: 7224.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E6
#5: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2 / Sphingosine
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS MH830353.1 FOR THE PROTEIN.

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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 E6 / Type: VIRUS / Entity ID: 1, 2, 3, 4 / Source: MULTIPLE SOURCES
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Echovirus E6
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 5.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
Image processingDetails: Cryo-EM structure of full Echovirus 6 particle at PH 5.5
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4321 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.0066671
f_angle_d0.9189094
f_dihedral_angle_d9.0053952
f_chiral_restr0.0591005
f_plane_restr0.0081182

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