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- EMDB-45304: Cryo-EM Structure of EV-D68 A2 Inactivated Virus Particle -

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Basic information

Entry
Database: EMDB / ID: EMD-45304
TitleCryo-EM Structure of EV-D68 A2 Inactivated Virus Particle
Map data
SampleEnterovirus != Human enterovirus D68

Enterovirus

  • Virus: Human enterovirus D68
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
KeywordsEV-D68 / B3 subclade / VLP / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / protein sequestering activity / 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 / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / protein sequestering activity / 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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host NF-kappaB cascade / RNA helicase activity / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / cytoplasm
Similarity search - Function
Picornavirus coat protein / 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) ...Picornavirus coat protein / 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) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman enterovirus D68
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsCheng J / Krug PW / Lei H / Moss DL / Huang R / Lang ZC / Morton AJ / Shen C / Pierson TC / Zhou T ...Cheng J / Krug PW / Lei H / Moss DL / Huang R / Lang ZC / Morton AJ / Shen C / Pierson TC / Zhou T / Ruckwardt TJ / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Cryo-EM Structures of EV-D68 Vaccine Candidates - Virus-like Particle and Inactivated Virus Particle
Authors: Cheng J / Krug PW / Lei H / Moss DL / Huang R / Lang ZC / Morton AJ / Shen C / Pierson TC / Zhou T / Ruckwardt TJ / Kwong PD
History
DepositionJun 12, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45304.png

Downloads & links

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Map

FileDownload / File: emd_45304.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 640 pix.
= 531.2 Å		0.83 Å/pix.
x 640 pix.
= 531.2 Å		0.83 Å/pix.
x 640 pix.
= 531.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.17540243 - 0.4649354
Average (Standard dev.)-0.0010507933 (±0.024391696)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 531.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45304_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45304_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Enterovirus

EntireName: Enterovirus
Components
  • Virus: Human enterovirus D68
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4

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Supramolecule #1: Human enterovirus D68

SupramoleculeName: Human enterovirus D68 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 42789 / Sci species name: Human enterovirus D68 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SUBSPECIES / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human enterovirus D68
Molecular weightTheoretical: 32.956465 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IESIIKTATD TVKSEINAEL GVVPSLNAVE TGASSNTEPE EAIQTRTVIN QHGVSETLVE NFLSRAALVS KRSFEYKNHT SSEARTDKN FYKWTINTKS FVQLRRKLEL FTYLRFDAEI TILTTVAVGS NNSTYMGLPD LTLQAMFVPT GALTPEKQDS F HWQSGSNA ...String:
IESIIKTATD TVKSEINAEL GVVPSLNAVE TGASSNTEPE EAIQTRTVIN QHGVSETLVE NFLSRAALVS KRSFEYKNHT SSEARTDKN FYKWTINTKS FVQLRRKLEL FTYLRFDAEI TILTTVAVGS NNSTYMGLPD LTLQAMFVPT GALTPEKQDS F HWQSGSNA SVFFKVSDPP ARMTIPFMCI NSAYSVFYDG FAGFEKNGLY GINPADTIGN LCVRIVNEHQ PIGFTVTVRV YM KPKHIKA WAPRPPRTLP YMSIANANYK GKERAPNALN AIIGNRESVK TMPHDIVLV

UniProtKB: Genome polyprotein

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Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human enterovirus D68
Molecular weightTheoretical: 27.624227 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SPSAEACGYS DRVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI DKPTQPETAT DRFYTLKSVK WETESTGWWW KLPDALNNI GMFGQNVQHH YLYRSGFLIH VQCNATKFHQ GALLVVAIPE HQRGAHNTTT SPGFDDIMKG EEGGTFNHPY V LDDGTSLA ...String:
SPSAEACGYS DRVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI DKPTQPETAT DRFYTLKSVK WETESTGWWW KLPDALNNI GMFGQNVQHH YLYRSGFLIH VQCNATKFHQ GALLVVAIPE HQRGAHNTTT SPGFDDIMKG EEGGTFNHPY V LDDGTSLA CATIFPHQWI NLRTNNSATI VLPWMNAAPM DFPLRHNQWT LAIIPVVPLG TRTVSSMVPI TVSIAPMCCE FN GLRHAIT Q

UniProtKB: Genome polyprotein

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Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human enterovirus D68
Molecular weightTheoretical: 27.282035 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GVPTYLLPGS GQFLTTDDHS SAPVLPCFNP TPEMHIPGQV RNMLEVIQVE SMMEINNTEN AVGMQRLKVD ISVLTDVDQL LFNIPLDIQ LDGPLRNTLV GNISRYYTHW SGSLEMTFMF CGSFMATGKL ILCYTPPGGS CPTTRETAML GTHIVWDFGL Q SSVTLVIP ...String:
GVPTYLLPGS GQFLTTDDHS SAPVLPCFNP TPEMHIPGQV RNMLEVIQVE SMMEINNTEN AVGMQRLKVD ISVLTDVDQL LFNIPLDIQ LDGPLRNTLV GNISRYYTHW SGSLEMTFMF CGSFMATGKL ILCYTPPGGS CPTTRETAML GTHIVWDFGL Q SSVTLVIP WISGSHYRMF NNDAKSTNAN VGYVTCFMQT NLIVPSESSN TCSLIGFVAA KDDFSLRLMR DSPDIGQLEH LH EAEAAYQ

UniProtKB: Genome polyprotein

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Macromolecule #4: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human enterovirus D68
Molecular weightTheoretical: 7.468157 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MGAQVTRQQT GTHENANIAT NGSHITYNQI NFYKDSYAAS ASKQDFSQDP SKFTEPVVEG LKAGAPVLK

UniProtKB: Genome polyprotein

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: 4D-STEM / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6wdt

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10000
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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