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- EMDB-65507: CryoEM structure of EV-D68 strain Fermon in complex with MFSD6-R1... -

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Basic information

Entry
Database: EMDB / ID: EMD-65507
TitleCryoEM structure of EV-D68 strain Fermon in complex with MFSD6-R196-L226-NAtreat
Map data
Sample
  • Complex: enterovirus D68
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: P1
    • Protein or peptide: Capsid protein VP4
    • Protein or peptide: Major facilitator superfamily domain-containing protein 6
    • Protein or peptide: Capsid protein VP1
  • Ligand: SPHINGOSINE
KeywordsEV-D68 / MFSD6 / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class I / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / protein sequestering activity / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class I / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / protein sequestering activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity / 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 / 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 / virion attachment to host cell / host cell nucleus / structural molecule activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Major facilitator superfamily associated domain / : / MFS_1 like family / MFS transporter superfamily / : / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain ...Major facilitator superfamily associated domain / : / MFS_1 like family / MFS transporter superfamily / : / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / 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 / Major facilitator superfamily domain-containing protein 6
Similarity search - Component
Biological speciesenterovirus D68 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsLiang SJ / Lou ZY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: CryoEM structure of EV-D68 strain Fermon in complex with MFSD6-R196-L226-NAtreat
Authors: Liang SJ / Lou ZY
History
DepositionJul 24, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65507.png

Downloads & links

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Map

FileDownload / File: emd_65507.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 224 pix.
= 208.544 Å		0.93 Å/pix.
x 224 pix.
= 208.544 Å		0.93 Å/pix.
x 224 pix.
= 208.544 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.931 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.47379178 - 0.71406394
Average (Standard dev.)0.007979395 (±0.05107998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 208.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65507_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_65507_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 D68

EntireName: enterovirus D68
Components
  • Complex: enterovirus D68
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: P1
    • Protein or peptide: Capsid protein VP4
    • Protein or peptide: Major facilitator superfamily domain-containing protein 6
    • Protein or peptide: Capsid protein VP1
  • Ligand: SPHINGOSINE

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Supramolecule #1: enterovirus D68

SupramoleculeName: enterovirus D68 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: enterovirus D68

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Macromolecule #1: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: enterovirus D68
Molecular weightTheoretical: 27.706336 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SPSAEACGYS DRVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI DKPTQPETST DRFYTLRSVK WESNSTGWWW KLPDALNNI GMFGQNVQYH YLYRSGFLIH VQCNATKFHQ GALLVVAIPE HQRGAHDTTT SPGFNDIMKG ERGGTFNHPY V LDDGTSIA ...String:
SPSAEACGYS DRVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI DKPTQPETST DRFYTLRSVK WESNSTGWWW KLPDALNNI GMFGQNVQYH YLYRSGFLIH VQCNATKFHQ GALLVVAIPE HQRGAHDTTT SPGFNDIMKG ERGGTFNHPY V LDDGTSIA CATIFPHQWI NLRTNNSATI VLPWMNVAPM DFPLRHNQWT LAVIPVVPLG TRTMSSVVPI TVSIAPMCCE FN GLRHAIT Q

UniProtKB: Genome polyprotein

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Macromolecule #2: P1

MacromoleculeName: P1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: enterovirus D68
Molecular weightTheoretical: 27.202881 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GVPTYLLPGS GQFLTTDDHS SAPVLPCFNP TPEMHIPGQI RNMLEMIQVE SMMEINNTDG ANGMERLRVD ISVQADLDQL LFNIPLDIQ LDGPLRNTLV GNISRYYTHW SGSLEMTFMF CGSFMATGKL ILCYTPPGGS CPTTRETAML GTHIVWDFGL Q SSITLIIP ...String:
GVPTYLLPGS GQFLTTDDHS SAPVLPCFNP TPEMHIPGQI RNMLEMIQVE SMMEINNTDG ANGMERLRVD ISVQADLDQL LFNIPLDIQ LDGPLRNTLV GNISRYYTHW SGSLEMTFMF CGSFMATGKL ILCYTPPGGS CPTTRETAML GTHIVWDFGL Q SSITLIIP WISGSHYRMF NSDAKSTNAN VGYVTCFMQT NLIVPSESSD TCSLIGFIAA KDDFSLRLMR DSPDIGQSNH LH GAEAAYQ

UniProtKB: Genome polyprotein

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Macromolecule #3: Capsid protein VP4

MacromoleculeName: Capsid protein VP4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: 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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Macromolecule #4: Major facilitator superfamily domain-containing protein 6

MacromoleculeName: Major facilitator superfamily domain-containing protein 6
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.514959 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
REKRNLLETR LNVSDTVTLP TAPNMNSEPT L

UniProtKB: Major facilitator superfamily domain-containing protein 6

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Macromolecule #5: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: enterovirus D68
Molecular weightTheoretical: 32.683066 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VESIIKTATD TVKSEINAEL GVVPSLNAVE TGATSNTEPE EAIQTRTVIN QHGVSETLVE NFLGRAALVS KKSFEYKNHA SSSAGTHKN FFKWTINTKS FVQLRRKLEL FTYLRFDAEI TILTTVAVNG NNDSTYMGLP DLTLQAMFVP TGALTPKEQD S FHWQSGSN ...String:
VESIIKTATD TVKSEINAEL GVVPSLNAVE TGATSNTEPE EAIQTRTVIN QHGVSETLVE NFLGRAALVS KKSFEYKNHA SSSAGTHKN FFKWTINTKS FVQLRRKLEL FTYLRFDAEI TILTTVAVNG NNDSTYMGLP DLTLQAMFVP TGALTPKEQD S FHWQSGSN ASVFFKISDP PARMTIPFMC INSAYSVFYD GFAGFEKNGL YGINPADTIG NLCVRIVNEH QPVGFTVTVR VY MKPKHIK AWAPRPPRTM PYMSIANANY KGRDTAPNTL NAIIGNRASV TTMPHNIVT

UniProtKB: Genome polyprotein

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Macromolecule #7: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 7 / Number of copies: 1 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 213459
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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