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- EMDB-0332: Structure of EV71 complexed with its receptor SCARB2 -

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Basic information

Entry
Database: EMDB / ID: EMD-0332
TitleStructure of EV71 complexed with its receptor SCARB2
Map data
Sample
  • Complex: complex of EV71 and SCARB2
    • Complex: SCARB2
      • Protein or peptide: Lysosome membrane protein 2
    • Virus: Enterovirus A71
      • Protein or peptide: PolyproteinProteolysis
      • Protein or peptide: PolyproteinProteolysis
      • Protein or peptide: PolyproteinProteolysis
      • Protein or peptide: PolyproteinProteolysis
  • Ligand: 1-(2-aminopyridin-4-yl)-3-[(3S)-5-{4-[(E)-(ethoxyimino)methyl]phenoxy}-3-methylpentyl]imidazolidin-2-one
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


regulation of glucosylceramide catabolic process / regulation of carbohydrate catabolic process / regulation of endosome organization / aminophospholipid transport / endosome to plasma membrane protein transport / regulation of lysosome organization / protein targeting to lysosome / scavenger receptor activity / phosphatidylcholine binding / cargo receptor activity ...regulation of glucosylceramide catabolic process / regulation of carbohydrate catabolic process / regulation of endosome organization / aminophospholipid transport / endosome to plasma membrane protein transport / regulation of lysosome organization / protein targeting to lysosome / scavenger receptor activity / phosphatidylcholine binding / cargo receptor activity / cholesterol binding / phosphatidylserine binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / receptor-mediated endocytosis / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / lysosomal lumen / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / sensory perception of sound / clathrin-coated endocytic vesicle membrane / positive regulation of neuron projection development / endocytic vesicle membrane / viral capsid / : / transmembrane signaling receptor activity / nucleoside-triphosphate phosphatase / Cargo recognition for clathrin-mediated endocytosis / virus receptor activity / protein complex oligomerization / Clathrin-mediated endocytosis / late endosome membrane / monoatomic ion channel activity / protein-folding chaperone binding / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / RNA helicase activity / DNA replication / endosome membrane / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / lysosomal membrane / viral RNA genome replication / cysteine-type endopeptidase activity / Golgi membrane / RNA-dependent RNA polymerase activity / focal adhesion / DNA-templated transcription / host cell nucleus / virion attachment to host cell / endoplasmic reticulum membrane / structural molecule activity / enzyme binding / protein homodimerization activity / proteolysis / RNA binding / extracellular exosome / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Lysosome membrane protein II / CD36 family / CD36 family / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A ...Lysosome membrane protein II / CD36 family / CD36 family / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Lysosome membrane protein 2 / Genome polyprotein / Polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human) / Enterovirus A71
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhou D / Zhao Y / Kotecha A / Fry EE / Kelly J / Wang X / Rao Z / Rowlands DJ / Ren J / Stuart DI
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N00065X/1 United Kingdom
CitationJournal: Nat Microbiol / Year: 2019
Title: Unexpected mode of engagement between enterovirus 71 and its receptor SCARB2.
Authors: Daming Zhou / Yuguang Zhao / Abhay Kotecha / Elizabeth E Fry / James T Kelly / Xiangxi Wang / Zihe Rao / David J Rowlands / Jingshan Ren / David I Stuart /
Abstract: Enterovirus 71 (EV71) is a common cause of hand, foot and mouth disease-a disease endemic especially in the Asia-Pacific region. Scavenger receptor class B member 2 (SCARB2) is the major receptor of ...Enterovirus 71 (EV71) is a common cause of hand, foot and mouth disease-a disease endemic especially in the Asia-Pacific region. Scavenger receptor class B member 2 (SCARB2) is the major receptor of EV71, as well as several other enteroviruses responsible for hand, foot and mouth disease, and plays a key role in cell entry. The isolated structures of EV71 and SCARB2 are known, but how they interact to initiate infection is not. Here, we report the EV71-SCARB2 complex structure determined at 3.4 Å resolution using cryo-electron microscopy. This reveals that SCARB2 binds EV71 on the southern rim of the canyon, rather than across the canyon, as predicted. Helices 152-163 (α5) and 183-193 (α7) of SCARB2 and the viral protein 1 (VP1) GH and VP2 EF loops of EV71 dominate the interaction, suggesting an allosteric mechanism by which receptor binding might facilitate the low-pH uncoating of the virus in the endosome/lysosome. Remarkably, many residues within the binding footprint are not conserved across SCARB2-dependent enteroviruses; however, a conserved proline and glycine seem to be key residues. Thus, although the virus maintains antigenic variability even within the receptor-binding footprint, the identification of binding 'hot spots' may facilitate the design of receptor mimic therapeutics less likely to quickly generate resistance.
History
DepositionNov 1, 2018-
Header (metadata) releaseNov 28, 2018-
Map releaseNov 28, 2018-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6i2k
  • Surface level: 0.0213
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6i2k
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0332.png

Downloads & links

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Map

FileDownload / File: emd_0332.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.0213 / Movie #1: 0.025
Minimum - Maximum-0.16716264 - 0.2783022
Average (Standard dev.)0.0015467653 (±0.01628007)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 540.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z540.000540.000540.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1670.2780.002

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Supplemental data

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Sample components

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Entire : complex of EV71 and SCARB2

EntireName: complex of EV71 and SCARB2
Components
  • Complex: complex of EV71 and SCARB2
    • Complex: SCARB2
      • Protein or peptide: Lysosome membrane protein 2
    • Virus: Enterovirus A71
      • Protein or peptide: PolyproteinProteolysis
      • Protein or peptide: PolyproteinProteolysis
      • Protein or peptide: PolyproteinProteolysis
      • Protein or peptide: PolyproteinProteolysis
  • Ligand: 1-(2-aminopyridin-4-yl)-3-[(3S)-5-{4-[(E)-(ethoxyimino)methyl]phenoxy}-3-methylpentyl]imidazolidin-2-one
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: complex of EV71 and SCARB2

SupramoleculeName: complex of EV71 and SCARB2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

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Supramolecule #3: SCARB2

SupramoleculeName: SCARB2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293

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Supramolecule #2: Enterovirus A71

SupramoleculeName: Enterovirus A71 / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 / NCBI-ID: 39054 / Sci species name: Enterovirus A71 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Polyprotein

MacromoleculeName: Polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus A71
Molecular weightTheoretical: 32.755766 KDa
SequenceString: GDRVADMIES SIGDSVSRAL TQALPAPTGQ NTQVSSHRLD TGEVPALQAA EIGASSNTSD ESMIETRCVL NSHSTAETTL DSFFSRAGL VGEIDLPLEG TTNPSGYANW DIDITGYAQM RRKVELFTYM RFDAEFTFVA CTPTGQVVPQ LLQYMFVPPG A PKPESRES ...String:
GDRVADMIES SIGDSVSRAL TQALPAPTGQ NTQVSSHRLD TGEVPALQAA EIGASSNTSD ESMIETRCVL NSHSTAETTL DSFFSRAGL VGEIDLPLEG TTNPSGYANW DIDITGYAQM RRKVELFTYM RFDAEFTFVA CTPTGQVVPQ LLQYMFVPPG A PKPESRES LAWQTATNPS VFVKLTDPPA QVSVPFMSPA SAYQWFYDGY PTFGEHKQEK DLEYGACPNN MMGTFSVRTV GS SKSKYAL VVRIYMRMKH VRAWIPRPMR NQNYLFKANP NYAGDSIKPT GTSRNAITTL

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Macromolecule #2: Polyprotein

MacromoleculeName: Polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus A71
Molecular weightTheoretical: 27.784213 KDa
SequenceString: SPSAEACGYS DRVAQLTIGN STITTQEAAN IIVGYGEWPS YCSDDDATAV DKPTRPDVSV NRFYTLDTKL WEKSSKGWYW KFPDVLTET GVFGQNAQFH YLYRSGFCIH VQCNASKFHQ GALLVAILPE YVIGTVAGGT GTEDSHPPYI QTQPGADGFE L QHPYVLDA ...String:
SPSAEACGYS DRVAQLTIGN STITTQEAAN IIVGYGEWPS YCSDDDATAV DKPTRPDVSV NRFYTLDTKL WEKSSKGWYW KFPDVLTET GVFGQNAQFH YLYRSGFCIH VQCNASKFHQ GALLVAILPE YVIGTVAGGT GTEDSHPPYI QTQPGADGFE L QHPYVLDA GIPISQLTVC PHQWINLRTN NCATIIVPYM NTLPFDSALN HCNFGLLVVP ISPLDFDQGA TPVIPITITL AP MCSEFAG LRQAVTQ

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Macromolecule #3: Polyprotein

MacromoleculeName: Polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus A71
Molecular weightTheoretical: 26.540332 KDa
SequenceString: GFPTELKPGT NQFLTTDDGV SAPILPNFHP TPCIHIPGEV RNLLELCQVE TILEVNNVPT NATSLMERLR FPVSAQAGKG ELCAVFRAD PGRDGPWQST MLGQLCGYYT QWSGSLEVTF MFTGSFMATG KMLIAYTPPG GPLPKDRATA MLGTHVIWDF G LQSSVTLV ...String:
GFPTELKPGT NQFLTTDDGV SAPILPNFHP TPCIHIPGEV RNLLELCQVE TILEVNNVPT NATSLMERLR FPVSAQAGKG ELCAVFRAD PGRDGPWQST MLGQLCGYYT QWSGSLEVTF MFTGSFMATG KMLIAYTPPG GPLPKDRATA MLGTHVIWDF G LQSSVTLV IPWISNTHYR AHARDGVFDY YTTGLVSIWY QTNYVVPIGA PNTAYIIALA AAQKNFTMKL CKDTSHILQT AS IQ

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Macromolecule #4: Polyprotein

MacromoleculeName: Polyprotein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus A71
Molecular weightTheoretical: 6.380943 KDa
SequenceString:
SHENSNSATE GSTINYTTIN YYKDSYAATA GKQSLKQDPD KFANPVKDIF TEMAAPLK

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Macromolecule #5: Lysosome membrane protein 2

MacromoleculeName: Lysosome membrane protein 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.72775 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ETGVFQKAVD QSIEKKIVLR NGTEAFDSWE KPPLPVYTQF YFFNVTNPEE ILRGETPRVE EVGPYTYREL RNKANIQFGD NGTTISAVS NKAYVFERDQ SVGDPKIDLI RTLNIPVLTV IEWSQVHFLR EIIEAMLKAY QQKLFVTHTV DELLWGYKDE I LSLIHVFR ...String:
ETGVFQKAVD QSIEKKIVLR NGTEAFDSWE KPPLPVYTQF YFFNVTNPEE ILRGETPRVE EVGPYTYREL RNKANIQFGD NGTTISAVS NKAYVFERDQ SVGDPKIDLI RTLNIPVLTV IEWSQVHFLR EIIEAMLKAY QQKLFVTHTV DELLWGYKDE I LSLIHVFR PDISPYFGLF YEKNGTNDGD YVFLTGEDSY LNFTKIVEWN GKTSLDWWIT DKCNMINGTD GDSFHPLITK DE VLYVFPS DFCRSVYITF SDYESVQGLP AFRYKVPAEI LANTSDNAGF CIPEGNCLGS GVLNVSICKN GAPIIMSFPH FYQ ADERFV SAIEGMHPNQ EDHETFVDIN PLTGIILKAA KRFQINIYVK KLDDFVETGD IRTMVFPVMY LNESVHIDKE TASR LKSMI NTTGKHHHHH H

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Macromolecule #11: 1-(2-aminopyridin-4-yl)-3-[(3S)-5-{4-[(E)-(ethoxyimino)methyl]phe...

MacromoleculeName: 1-(2-aminopyridin-4-yl)-3-[(3S)-5-{4-[(E)-(ethoxyimino)methyl]phenoxy}-3-methylpentyl]imidazolidin-2-one
type: ligand / ID: 11 / Number of copies: 1 / Formula: 906
Molecular weightTheoretical: 425.524 Da
Chemical component information

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

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Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 5.1
VitrificationCryogen name: ETHANE
Detailsvirus particle/SCARB2 ratio: 1:100

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 757 / Average electron dose: 35.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3vbh

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionNumber classes used: 4 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 10443
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

3vbh

,

4q4b

)
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 150
Output model

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

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