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- EMDB-7635: CryoEM structure of human enterovirus D68 emptied particle (after... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7635 | |||||||||
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Title | CryoEM structure of human enterovirus D68 emptied particle (after incubation with low molecular weight heparin) | |||||||||
![]() | sharpened map in which the inner density is masked out | |||||||||
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![]() | virus / genome release / receptor | |||||||||
Function / homology | ![]() picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization ...picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.03 Å | |||||||||
![]() | Liu Y / Rossmann MG | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Bypassing pan-enterovirus host factor PLA2G16. Authors: Jim Baggen / Yue Liu / Heyrhyoung Lyoo / Arno L W van Vliet / Maryam Wahedi / Jost W de Bruin / Richard W Roberts / Pieter Overduin / Adam Meijer / Michael G Rossmann / Hendrik Jan Thibaut / ...Authors: Jim Baggen / Yue Liu / Heyrhyoung Lyoo / Arno L W van Vliet / Maryam Wahedi / Jost W de Bruin / Richard W Roberts / Pieter Overduin / Adam Meijer / Michael G Rossmann / Hendrik Jan Thibaut / Frank J M van Kuppeveld / ![]() ![]() Abstract: Enteroviruses are a major cause of human disease. Adipose-specific phospholipase A2 (PLA2G16) was recently identified as a pan-enterovirus host factor and potential drug target. In this study, we ...Enteroviruses are a major cause of human disease. Adipose-specific phospholipase A2 (PLA2G16) was recently identified as a pan-enterovirus host factor and potential drug target. In this study, we identify a possible mechanism of PLA2G16 evasion by employing a dual glycan receptor-binding enterovirus D68 (EV-D68) strain. We previously showed that this strain does not strictly require the canonical EV-D68 receptor sialic acid. Here, we employ a haploid screen to identify sulfated glycosaminoglycans (sGAGs) as its second glycan receptor. Remarkably, engagement of sGAGs enables this virus to bypass PLA2G16. Using cryo-EM analysis, we reveal that, in contrast to sialic acid, sGAGs stimulate genome release from virions via structural changes that enlarge the putative openings for genome egress. Together, we describe an enterovirus that can bypass PLA2G16 and identify additional virion destabilization as a potential mechanism to circumvent PLA2G16. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 156.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.9 KB 20.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.5 KB | Display | ![]() |
Images | ![]() | 280 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Others | ![]() ![]() | 57.5 MB 57.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6cv4MC ![]() 7632C ![]() 7633C ![]() 7634C ![]() 7636C ![]() 7638C ![]() 6cv1C ![]() 6cv2C ![]() 6cv3C ![]() 6cv5C ![]() 6cvbC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | sharpened map in which the inner density is masked out | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: unsharpened half map in which the inner density is retained
File | emd_7635_half_map_1.map | ||||||||||||
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Annotation | unsharpened half map in which the inner density is retained | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: unsharpened half map in which the inner density is retained
File | emd_7635_half_map_2.map | ||||||||||||
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Annotation | unsharpened half map in which the inner density is retained | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Enterovirus D68
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Enterovirus D68
Supramolecule | Name: Enterovirus D68 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 42789 / Sci species name: Enterovirus D68 / Sci species strain: 947 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: ![]() |
-Macromolecule #1: viral protein 1
Macromolecule | Name: viral protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 32.957449 KDa |
Sequence | String: IESIIKTATD TVKSEINAEL GVVPSLNAVE TGATSNTEPE EAIQTRTVIN QHGVSETLVE NFLSRAALVS KRSFEYKDHT SSAAQTDKN FFKWTINTRS FVQLRRKLEL FTYLRFDAEI TILTTVAVNG SSNNTYMGLP NLTLQAMFVP TGALTPEKQD S FHWQSGSN ...String: IESIIKTATD TVKSEINAEL GVVPSLNAVE TGATSNTEPE EAIQTRTVIN QHGVSETLVE NFLSRAALVS KRSFEYKDHT SSAAQTDKN FFKWTINTRS FVQLRRKLEL FTYLRFDAEI TILTTVAVNG SSNNTYMGLP NLTLQAMFVP TGALTPEKQD S FHWQSGSN ASVFFKISDP PARMTIPFMC INSAYSVFYD GFAGFEKSGL YGINPADTIG NLCVRIVNEH QPVGFTVTVR VY MKPKHIK AWAPRPPRTL PYMSIANANY KGKKRAPNAL NAIIGNRDSV KTMPHNIVTT UniProtKB: Genome polyprotein |
-Macromolecule #2: viral protein 3
Macromolecule | Name: viral protein 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 27.170895 KDa |
Sequence | String: GVPTYLLPGS GQFLTTDDHS SAPVLPCFNP TPEMHIPGQV RNMLEVVQVE SMMEINNTES AVGMERLKVD ISALTDVDQL LFNIPLDIQ LDGPLRNTLV GNISRYYTHW SGSLEMTFMF CGSFMATGKL ILCYTPPGGS CPTTRETAML GTHIVWDFGL Q SSVTLIIP ...String: GVPTYLLPGS GQFLTTDDHS SAPVLPCFNP TPEMHIPGQV RNMLEVVQVE SMMEINNTES AVGMERLKVD ISALTDVDQL LFNIPLDIQ LDGPLRNTLV GNISRYYTHW SGSLEMTFMF CGSFMATGKL ILCYTPPGGS CPTTRETAML GTHIVWDFGL Q SSVTLIIP WISGSHYRMF NNDAKSTNAN VGYVTCFMQT NLIVPSESSD TCSLIGFIAA KDDFSLRLMR DSPDIGQIDH LH AAEAAYQ UniProtKB: Genome polyprotein |
-Macromolecule #3: viral protein 2
Macromolecule | Name: viral protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 27.595215 KDa |
Sequence | String: SPSAEACGYS DRVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI DKPTQPETAT DRFYTLKSVK WEAGSTGWWW KLPDALNNI GMFGQNVQHH YLYRSGFLIH VQCNATRFHQ GALLVVAIPE HQRGAHNTNT SPGFDDIMKG EEGGTFNHPY V LDDGTSLA ...String: SPSAEACGYS DRVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI DKPTQPETAT DRFYTLKSVK WEAGSTGWWW KLPDALNNI GMFGQNVQHH YLYRSGFLIH VQCNATRFHQ GALLVVAIPE HQRGAHNTNT SPGFDDIMKG EEGGTFNHPY V LDDGTSLA CATIFPHQWI NLRTNNSATI VLPWMNAAPM DFPLRHNQWT LAIIPVVPLG TRTMSSMVPI TVSIAPMCCE FN GLRHAIT Q UniProtKB: Genome polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.2 / Details: phosphate buffer |
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Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Pressure: 0.02 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 2-35 / Number grids imaged: 1 / Number real images: 872 / Average exposure time: 7.0 sec. / Average electron dose: 33.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 4.5 µm / Calibrated defocus min: 0.6 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient |
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Output model | ![]() PDB-6cv4: |