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- PDB-6ilj: Cryo-EM structure of Echovirus 6 complexed with its attachment re... -

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Basic information

Entry
Database: PDB / ID: 6ilj
TitleCryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 5.5
Components
  • (Capsid protein ...Capsid) x 4
  • Complement decay-accelerating factor
KeywordsVIRUS / Echovirus 6 / CD55 / Cryo-EM / virus-receptor complex
Function / homology
Function and homology information


Regulation of Complement cascade / COPI-mediated anterograde transport / Class B/2 (Secretin family receptors) / Neutrophil degranulation / positive regulation of CD4-positive, alpha-beta T cell activation / CD4-positive, alpha-beta T cell cytokine production / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of lipopolysaccharide-mediated signaling pathway / respiratory burst ...Regulation of Complement cascade / COPI-mediated anterograde transport / Class B/2 (Secretin family receptors) / Neutrophil degranulation / positive regulation of CD4-positive, alpha-beta T cell activation / CD4-positive, alpha-beta T cell cytokine production / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of lipopolysaccharide-mediated signaling pathway / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell proliferation / ficolin-1-rich granule membrane / secretory granule membrane / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / anchored component of membrane / complement activation, classical pathway / regulation of complement activation / virus receptor activity / positive regulation of cytosolic calcium ion concentration / endoplasmic reticulum to Golgi vesicle-mediated transport / lipid binding / membrane raft / Golgi membrane / innate immune response / neutrophil degranulation / cell surface / extracellular exosome / extracellular region / plasma membrane
Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP domain / Sushi repeat (SCR repeat)
Complement decay-accelerating factor
Specimen sourceHomo sapiens (human)
Echovirus E6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 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 Echovirus 6 complexed with its attachment receptor CD55 at PH 5.5
Authors: Liu, S. / Peng, R. / Zhao, X. / George, F.G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 18, 2018 / Release: May 15, 2019Array

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-9684
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  • Superimposition on EM map
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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
E: Complement decay-accelerating factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0966
Polymers114,7975
Non-polymers2991
Water0
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: Complement decay-accelerating factor
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)6,905,775360
Polymers6,887,806300
Non-polymers17,97060
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area22980 Å2
ΔGint-102 kcal/mol
Surface area45880 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
E: Complement decay-accelerating factor
hetero molecules
x 5


  • icosahedral pentamer
  • 575 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)575,48130
Polymers573,98425
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
E: Complement decay-accelerating factor
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 691 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)690,57836
Polymers688,78130
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

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Capsid protein ... , 4 types, 4 molecules ABCD

#1: Protein/peptide Capsid protein VP1 /


Mass: 31707.332 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: 7338.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E6

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Protein/peptide / Non-polymers , 2 types, 2 molecules E

#5: Protein/peptide Complement decay-accelerating factor


Mass: 21307.959 Da / Num. of mol.: 1 / Fragment: UNP residues 94-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD55, CR, DAF / Cell (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: P08174
#6: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2 / Sphingosine

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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: Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 5.5
Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5 / Source: MULTIPLE SOURCES
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Echovirus E6
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
CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11494 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.0078240
f_angle_d0.93211231
f_dihedral_angle_d10.7774910
f_chiral_restr0.0591227
f_plane_restr0.0081465

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