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- EMDB-21647: Enterovirus D68 in complex with human monoclonal antibody EV68-159 -

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Basic information

Entry
Database: EMDB / ID: EMD-21647
TitleEnterovirus D68 in complex with human monoclonal antibody EV68-159Enterovirus 68
Map dataEnterovirus D68 in complex with human monoclonal antibody EV68-159Enterovirus 68
Sample
  • Complex: Enterovirus D68 in complex with human monoclonal antibody EV68-159Enterovirus 68
    • Complex: human antibody EV68-159
      • Protein or peptide: EV68-159 light chain
      • Protein or peptide: EV68-159 heavy chain
    • Virus: Enterovirus D68
      • Protein or peptide: viral protein 1
      • Protein or peptide: viral protein 2
      • Protein or peptide: viral protein 3
      • Protein or peptide: viral protein 4
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 / viral capsid ...: / 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 / viral capsid / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / peptidase activity / host cell cytoplasm / RNA helicase activity / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
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) ...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. / 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 speciesHomo sapiens (human) / Enterovirus D68
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsFu J / Klose T / Vogt MR / Crowe JE / Rossmann MG / Kuhn RJ / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI117905 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI104317 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01 HL070831 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI011219 United States
CitationJournal: Sci Immunol / Year: 2020
Title: Human antibodies neutralize enterovirus D68 and protect against infection and paralytic disease.
Authors: Matthew R Vogt / Jianing Fu / Nurgun Kose / Lauren E Williamson / Robin Bombardi / Ian Setliff / Ivelin S Georgiev / Thomas Klose / Michael G Rossmann / Yury A Bochkov / James E Gern / ...Authors: Matthew R Vogt / Jianing Fu / Nurgun Kose / Lauren E Williamson / Robin Bombardi / Ian Setliff / Ivelin S Georgiev / Thomas Klose / Michael G Rossmann / Yury A Bochkov / James E Gern / Richard J Kuhn / James E Crowe /
Abstract: Enterovirus D68 (EV-D68) causes outbreaks of respiratory illness, and there is increasing evidence that it causes outbreaks of acute flaccid myelitis (AFM). There are no licensed therapies to prevent ...Enterovirus D68 (EV-D68) causes outbreaks of respiratory illness, and there is increasing evidence that it causes outbreaks of acute flaccid myelitis (AFM). There are no licensed therapies to prevent or treat EV-D68 infection or AFM disease. We isolated a panel of EV-D68-reactive human monoclonal antibodies that recognize diverse antigenic variants from participants with prior infection. One potently neutralizing cross-reactive antibody, EV68-228, protected mice from respiratory and neurologic disease when given either before or after infection. Cryo-electron microscopy studies revealed that EV68-228 and another potently neutralizing antibody (EV68-159) bound around the fivefold or threefold axes of symmetry on virion particles, respectively. The structures suggest diverse mechanisms of action by these antibodies. The high potency and effectiveness observed in vivo suggest that antibodies are a mechanistic correlate of protection against AFM disease and are candidates for clinical use in humans with EV-D68 infection.
History
DepositionApr 1, 2020-
Header (metadata) releaseJul 15, 2020-
Map releaseJul 15, 2020-
UpdateJul 15, 2020-
Current statusJul 15, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 25
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wds
  • Surface level: 25
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6wds
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21647.png

Downloads & links

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Map

FileDownload / File: emd_21647.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEnterovirus D68 in complex with human monoclonal antibody EV68-159
Voxel sizeX=Y=Z: 0.874 Å
Density
Contour LevelBy AUTHOR: 25 / Movie #1: 25
Minimum - Maximum-95.65972 - 131.52507
Average (Standard dev.)0.052712336 (±4.608262)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 671.232 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8740.8740.874
M x/y/z768768768
origin x/y/z0.0000.0000.000
length x/y/z671.232671.232671.232
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS768768768
D min/max/mean-95.660131.5250.053

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Supplemental data

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Sample components

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Entire : Enterovirus D68 in complex with human monoclonal antibody EV68-159

EntireName: Enterovirus D68 in complex with human monoclonal antibody EV68-159Enterovirus 68
Components
  • Complex: Enterovirus D68 in complex with human monoclonal antibody EV68-159Enterovirus 68
    • Complex: human antibody EV68-159
      • Protein or peptide: EV68-159 light chain
      • Protein or peptide: EV68-159 heavy chain
    • Virus: Enterovirus D68
      • Protein or peptide: viral protein 1
      • Protein or peptide: viral protein 2
      • Protein or peptide: viral protein 3
      • Protein or peptide: viral protein 4

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Supramolecule #1: Enterovirus D68 in complex with human monoclonal antibody EV68-159

SupramoleculeName: Enterovirus D68 in complex with human monoclonal antibody EV68-159
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #3: human antibody EV68-159

SupramoleculeName: human antibody EV68-159 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1, #6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster) / Recombinant cell: CHO

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Supramolecule #2: Enterovirus D68

SupramoleculeName: Enterovirus D68 / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #2-#5 / NCBI-ID: 42789 / Sci species name: Enterovirus D68 / Sci species strain: US/MO/14-18947 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host systemOrganism: Homo sapiens (human) / Recombinant cell: RD

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Macromolecule #1: EV68-159 light chain

MacromoleculeName: EV68-159 light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.715928 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QSVLTQPPSA SGTPGQRVTI SCSGSSSNIE YNYVYWYQKF PGTAPKLLIY KNNQRPSGVP DRFSGSKSGT SASLAISGLR SEDEGDYYC AAWDDILSGV VFGGGTKLTV L

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Macromolecule #2: viral protein 1

MacromoleculeName: viral protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus D68 / Strain: US/MO/14-18047
Molecular weightTheoretical: 32.920309 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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

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Macromolecule #3: viral protein 2

MacromoleculeName: viral protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus D68 / Strain: US/MO/14-18047
Molecular weightTheoretical: 27.567135 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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

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Macromolecule #4: viral protein 3

MacromoleculeName: viral protein 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus D68 / Strain: US/MO/14-18047
Molecular weightTheoretical: 27.112814 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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

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Macromolecule #5: viral protein 4

MacromoleculeName: viral protein 4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus D68 / Strain: US/MO/14-18047
Molecular weightTheoretical: 7.33696 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GAQVTRQQTG THENANIATN GSHITYNQIN FYKDSYAASA SKQDFSQDPS KFTEPVVEGL KAGAPVLK

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Macromolecule #6: EV68-159 heavy chain

MacromoleculeName: EV68-159 heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.003529 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EVQLVESGGG LVKPGGLRLS CAASGFTFST YIMTWVRQAP GRGLEWVSSI STSSVYTFYA DSLKGRFTIS RDNAKNSVYL QMNSLRADD TAVYYCAREE GFRAYNLYWG QGTLVTVSS

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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: 8
GridMaterial: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 81000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 732 / Average exposure time: 12.0 sec. / Average electron dose: 31.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 42078
CTF correctionSoftware - Name: CTFFIND
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: jspr
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: OTHER / Software - Name: jspr
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: J3DR / Number images used: 30554
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4wm8

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6wds:
Enterovirus D68 in complex with human monoclonal antibody EV68-159

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