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- EMDB-31056: EV-D68 in complex with 8F12 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-31056
TitleEV-D68 in complex with 8F12 Fab
Map data8f12
Sample
  • Complex: Enterovirus D68 in complex with 8F12 Fab
    • Complex: 8F12 Fab
      • Protein or peptide: 8F12 Fab light chain
      • Protein or peptide: 8F12 Fab heavy chain
    • Virus: Enterovirus D68
      • Protein or peptide: Capsid protein VP1
      • Protein or peptide: Capsid protein VP3
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Capsid protein VP4
KeywordsEnterovirus D68 / Monoclonal antibody / Uncoating / VIRUS
Function / homology
Function and homology information


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 / channel 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / symbiont-mediated suppression of host innate immune response / 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
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
Biological speciesMus musculus (house mouse) / Human enterovirus D68 / Enterovirus D68
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsXu C / Cong Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2021
Title: Functional and structural characterization of a two-MAb cocktail for delayed treatment of enterovirus D68 infections.
Authors: Chao Zhang / Cong Xu / Wenlong Dai / Yifan Wang / Zhi Liu / Xueyang Zhang / Xuesong Wang / Haikun Wang / Sitang Gong / Yao Cong / Zhong Huang /
Abstract: Enterovirus D68 (EV-D68) is an emerging pathogen associated with respiratory diseases and/or acute flaccid myelitis. Here, two MAbs, 2H12 and 8F12, raised against EV-D68 virus-like particle (VLP), ...Enterovirus D68 (EV-D68) is an emerging pathogen associated with respiratory diseases and/or acute flaccid myelitis. Here, two MAbs, 2H12 and 8F12, raised against EV-D68 virus-like particle (VLP), show distinct preference in binding VLP and virion and in neutralizing different EV-D68 strains. A combination of 2H12 and 8F12 exhibits balanced and potent neutralization effects and confers broader protection in mice than single MAbs when given at onset of symptoms. Cryo-EM structures of EV-D68 virion complexed with 2H12 or 8F12 show that both antibodies bind to the canyon region of the virion, creating steric hindrance for sialic acid receptor binding. Additionally, 2H12 binding can impair virion integrity and trigger premature viral uncoating. We also capture an uncoating intermediate induced by 2H12 binding, not previously described for picornaviruses. Our study elucidates the structural basis and neutralizing mechanisms of the 2H12 and 8F12 MAbs and supports further development of the 2H12/8F12 cocktail as a broad-spectrum therapeutic agent against EV-D68 infections in humans.
History
DepositionMar 11, 2021-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ec5
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ec5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31056.png

Downloads & links

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Map

FileDownload / File: emd_31056.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation8f12
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 432 pix.
= 569.376 Å		1.32 Å/pix.
x 432 pix.
= 569.376 Å		1.32 Å/pix.
x 432 pix.
= 569.376 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.318 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.08446543 - 0.13827081
Average (Standard dev.)-0.000011774724 (±0.0072561773)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 569.376 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3181.3181.318
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z569.376569.376569.376
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.0840.138-0.000

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Supplemental data

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Sample components

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Entire : Enterovirus D68 in complex with 8F12 Fab

EntireName: Enterovirus D68 in complex with 8F12 Fab
Components
  • Complex: Enterovirus D68 in complex with 8F12 Fab
    • Complex: 8F12 Fab
      • Protein or peptide: 8F12 Fab light chain
      • Protein or peptide: 8F12 Fab heavy chain
    • Virus: Enterovirus D68
      • Protein or peptide: Capsid protein VP1
      • Protein or peptide: Capsid protein VP3
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Capsid protein VP4

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Supramolecule #1: Enterovirus D68 in complex with 8F12 Fab

SupramoleculeName: Enterovirus D68 in complex with 8F12 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: 8F12 Fab

SupramoleculeName: 8F12 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: Enterovirus D68

SupramoleculeName: Enterovirus D68 / type: virus / ID: 3 / Parent: 1 / Macromolecule list: #3-#6 / NCBI-ID: 42789 / Sci species name: Enterovirus D68 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: 8F12 Fab light chain

MacromoleculeName: 8F12 Fab light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.384848 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QIVLTQSPAA MSASPGEKVT MTCSASSSVI YMYWYQQKPG SSPRLLIYDT SNLASGVPVR FSGSGSGTSY SLTISRMEAE DAATYYCQQ WSSFPYTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK ...String:
QIVLTQSPAA MSASPGEKVT MTCSASSSVI YMYWYQQKPG SSPRLLIYDT SNLASGVPVR FSGSGSGTSY SLTISRMEAE DAATYYCQQ WSSFPYTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK DSTYSMSSTL TLTKDEYERH NSYTCEATHK TSTSPIVKSF NRNEC

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Macromolecule #2: 8F12 Fab heavy chain

MacromoleculeName: 8F12 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.233893 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQQPGTE LVRPGASVKL SCKASGYSFT SYWMNWVKQR PGQGLEWIGM IHPSDSETRL NQRFKDKATL TVDKSSNTAY MQLSSPTSE DSAVYYCARE GYDYDGFAYW GQGTLVTVSA AKTTPPSVYP LAPGCGDTTG SSVTLGCLVK GYFPESVTVT W NSGSLSSS ...String:
QVQLQQPGTE LVRPGASVKL SCKASGYSFT SYWMNWVKQR PGQGLEWIGM IHPSDSETRL NQRFKDKATL TVDKSSNTAY MQLSSPTSE DSAVYYCARE GYDYDGFAYW GQGTLVTVSA AKTTPPSVYP LAPGCGDTTG SSVTLGCLVK GYFPESVTVT W NSGSLSSS VHTFPALLQS GLYTMSSSVT VPSSTWPSQT VTCSVAHPAS STTVDKKL

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Macromolecule #3: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human enterovirus D68
Molecular weightTheoretical: 32.920309 KDa
SequenceString: IESIIKTATD TVKSEINAEL GVVPSLNAVE TGATSNTEPE EAIQTRTVIN QHGVSETLVE NFLSRAALVS KRSFEYKDHT SSTARADKN FFKWTINTRS FVQLRRKLEL FTYLRFDAEI TILTTVAVNG SGNNTYVGLP DLTLQAMFVP TGALTPEKQD S FHWQSGSN ...String:
IESIIKTATD TVKSEINAEL GVVPSLNAVE TGATSNTEPE EAIQTRTVIN QHGVSETLVE NFLSRAALVS KRSFEYKDHT SSTARADKN FFKWTINTRS FVQLRRKLEL FTYLRFDAEI TILTTVAVNG SGNNTYVGLP DLTLQAMFVP TGALTPEKQD S FHWQSGSN ASVFFKISDP PARITIPFMC INSAYSVFYD GFAGFEKNGL YGINPADTIG NLCVRIVNEH QPVGFTVTVR VY MKPKHIK AWAPRPPRTL PYMSIANANY KGKERAPNAL SAIIGNRDSV KTMPHNIVNT

UniProtKB: Genome polyprotein

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Macromolecule #4: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human enterovirus D68
Molecular weightTheoretical: 27.112814 KDa
SequenceString: GVPTYLLPGS GQFLTTDDHS SAPALPCFNP TPEMHIPGQV RNMLEVVQVE SMMEINNTES AVGMERLKVD ISALTDVDQL LFNIPLDIQ LDGPLRNTLV GNISRYYTHW SGSLEMTFMF CGSFMAAGKL ILCYTPPGGS CPTTRETAML GTHIVWDFGL Q SSVTLIIP ...String:
GVPTYLLPGS GQFLTTDDHS SAPALPCFNP TPEMHIPGQV RNMLEVVQVE SMMEINNTES AVGMERLKVD ISALTDVDQL LFNIPLDIQ LDGPLRNTLV GNISRYYTHW SGSLEMTFMF CGSFMAAGKL ILCYTPPGGS CPTTRETAML GTHIVWDFGL Q SSVTLIIP WISGSHYRMF NNDAKSTNAN VGYVTCFMQT NLIVPSESSD TCSLIGFIAA KDDFSLRLMR DSPDIGQLDH LH AAEAAYQ

UniProtKB: Genome polyprotein

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Macromolecule #5: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Human enterovirus D68
Molecular weightTheoretical: 27.567135 KDa
SequenceString: SPSAEACGYS DRVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI DKPTQPETAT DRFYTLKSVK WETGSTGWWW KLPDALNNI GMFGQNVQHH YLYRSGFLIH VQCNATKFHQ GALLVVAIPE HQRGAHNTNT SPGFDDIMKG EEGGTFNHPY V LDDGTSLA ...String:
SPSAEACGYS DRVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI DKPTQPETAT DRFYTLKSVK WETGSTGWWW KLPDALNNI GMFGQNVQHH YLYRSGFLIH VQCNATKFHQ GALLVVAIPE HQRGAHNTNT SPGFDDIMKG EEGGTFNHPY V LDDGTSLA CATIFPHQWI NLRTNNSATI VLPWMNAAPM DFPLRHNQWT LAIIPVVPLG TRTTSSMVPI TVSIAPMCCE FN GLRHAIT Q

UniProtKB: Genome polyprotein

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Macromolecule #6: Capsid protein VP4

MacromoleculeName: Capsid protein VP4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human enterovirus D68
Molecular weightTheoretical: 7.33696 KDa
SequenceString:
GAQVTRQQTG THENANIATN GSHITYNQIN FYKDSYAASA SKQDFSQDPS KFTEPVVEGL KAGAPVLK

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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30540
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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