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- PDB-6i2k: Structure of EV71 complexed with its receptor SCARB2 -

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Basic information

Entry
Database: PDB / ID: 6i2k
TitleStructure of EV71 complexed with its receptor SCARB2
Components
  • (PolyproteinProteolysis) x 4
  • Lysosome membrane protein 2
KeywordsVIRUS / Enterovirus 71 / SCARB2 / Hand-foot-mouth disease / EV71 receptor
Function / homologyCD36 family / Picornavirus coat protein (VP4) / Picornavirus/Calicivirus coat protein / Picornavirus coat protein VP4 superfamily / Picornavirus coat protein VP4 / picornavirus capsid protein / Lysosome membrane protein II / Viral coat protein subunit / CD36 family / Cargo recognition for clathrin-mediated endocytosis ...CD36 family / Picornavirus coat protein (VP4) / Picornavirus/Calicivirus coat protein / Picornavirus coat protein VP4 superfamily / Picornavirus coat protein VP4 / picornavirus capsid protein / Lysosome membrane protein II / Viral coat protein subunit / CD36 family / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / Picornavirus capsid / regulation of glucosylceramidase activity / regulation of endosome organization / regulation of lysosome organization / production of molecular mediator involved in inflammatory response / protein targeting to lysosome / regulation of lipopolysaccharide-mediated signaling pathway / scavenger receptor activity / action potential / late endosome membrane / clathrin-coated vesicle membrane / fatty acid metabolic process / positive regulation of neuron projection development / lysosomal lumen / phagocytosis, engulfment / virus receptor activity / lysosomal membrane / viral capsid / membrane organization / transmembrane signaling receptor activity / endosome membrane / Golgi membrane / focal adhesion / endoplasmic reticulum membrane / structural molecule activity / cell surface / enzyme binding / extracellular exosome / membrane / integral component of membrane / plasma membrane / Polyprotein / Polyprotein / Lysosome membrane protein 2 / Polyprotein
Function and homology information
Specimen sourceHomo sapiens (human)
Enterovirus A71
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.4 Å resolution
AuthorsZhou, D. / Zhao, Y. / Kotecha, A. / Fry, E.E. / Kelly, J. / Wang, X. / Rao, Z. / Rowlands, D.J. / Ren, J. / Stuart, D.I.
CitationJournal: To Be Published
Title: Unexpected mode of engagement between enterovirus 71 and its receptor SCARB2
Authors: Zhou, D. / Zhao, Y. / Kotecha, A. / Fry, E.E. / Kelly, J. / Wang, X. / Rao, Z. / Rowlands, D.J. / Ren, J. / Stuart, D.I.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 1, 2018 / Release: Nov 28, 2018

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Structure visualization

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  • 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
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Polyprotein
B: Polyprotein
C: Polyprotein
D: Polyprotein
E: Lysosome membrane protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,41435
Polyers141,1895
Non-polymers6,22530
Water0
1
A: Polyprotein
B: Polyprotein
C: Polyprotein
D: Polyprotein
E: Lysosome membrane protein 2
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,844,8272100
Polyers8,471,340300
Non-polymers373,4871800
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Polyprotein
B: Polyprotein
C: Polyprotein
D: Polyprotein
E: Lysosome membrane protein 2
hetero molecules
x 5


  • icosahedral pentamer
  • 737 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)737,069175
Polyers705,94525
Non-polymers31,124150
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Polyprotein
B: Polyprotein
C: Polyprotein
D: Polyprotein
E: Lysosome membrane protein 2
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 884 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)884,483210
Polyers847,13430
Non-polymers37,349180
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

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Components

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Protein/peptide , 5 types, 5 molecules ABCDE

#1: Protein/peptide Polyprotein / Proteolysis


Mass: 32755.766 Da / Num. of mol.: 1 / Source: (natural) Enterovirus A71
#2: Protein/peptide Polyprotein / Proteolysis


Mass: 27784.213 Da / Num. of mol.: 1 / Source: (natural) Enterovirus A71 / References: UniProt: D4QGA2
#3: Protein/peptide Polyprotein / Proteolysis


Mass: 26540.332 Da / Num. of mol.: 1 / Source: (natural) Enterovirus A71 / References: UniProt: D4QGA3
#4: Protein/peptide Polyprotein / Proteolysis


Mass: 6380.943 Da / Num. of mol.: 1 / Source: (natural) Enterovirus A71 / References: UniProt: Q6YLE3
#5: Protein/peptide Lysosome membrane protein 2 / 85 kDa lysosomal membrane sialoglycoprotein / LGP85 / CD36 antigen-like 2 / Lysosome membrane protein II / LIMP II / Scavenger receptor class B member 2


Mass: 47727.750 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: SCARB2, CD36L2, LIMP2, LIMPII / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q14108

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Non-polymers , 4 types, 30 molecules

#6: Chemical ChemComp-906 / 1-(2-aminopyridin-4-yl)-3-[(3S)-5-{4-[(E)-(ethoxyimino)methyl]phenoxy}-3-methylpentyl]imidazolidin-2-one


Mass: 425.524 Da / Num. of mol.: 1 / Formula: C23H31N5O3
#7: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 14 / Formula: C8H15NO6 / N-Acetylglucosamine
#8: Chemical
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 4 / Formula: C6H12O6
#9: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 11 / Formula: C6H12O6

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1complex of EV71 and SCARB2COMPLEX1, 2, 3, 4, 50MULTIPLE SOURCES
2Enterovirus A71VIRUS1, 2, 3, 41NATURAL
3SCARB2COMPLEX51RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
1239054Enterovirus A71
239606Homo sapiens (human)
Source (recombinant)Cell: HEK293 / Organism: Homo sapiens (human)
Details of virusEmpty: YES / Enveloped: NO / Virus isolate: OTHER / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 5.1
SpecimenConc.: 0.6 mg/ml / Details: virus particle/SCARB2 ratio: 1:100 / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 35 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 757

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
1EMAN2particle selection
4CTFFIND3CTF correction
7UCSF Chimeramodel fitting
11RELION2classification
12RELION23D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 10443 / Number of class averages: 4 / Symmetry type: POINT
Atomic model buildingOverall b value: 150 / Ref protocol: RIGID BODY FIT / Ref space: REAL
Atomic model building
IDPDB-ID 3D fitting ID
13VBH1
24Q4B1

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