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

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Basic information

Entry
Database: PDB / ID: 6wds
TitleEnterovirus D68 in complex with human monoclonal antibody EV68-159
Components
  • (viral protein ...) x 4
  • EV68-159 heavy chain
  • EV68-159 light chain
KeywordsVIRUS/IMMUNE SYSTEM / virus / enterovirus / antibody / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / VIRUS-IMMUNE SYSTEM complex
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 / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Jelly Rolls - #20 / 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 ...Jelly Rolls - #20 / 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 / Jelly Rolls / 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 / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterovirus D68
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsFu, J. / Klose, T. / Vogt, M.R. / Crowe, J.E. / Rossmann, M.G. / Kuhn, R.J. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI117905 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)U19 AI104317 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, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-21647
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  • Superimposition on EM map
  • EMDB-21647
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
L: EV68-159 light chain
A: viral protein 1
B: viral protein 2
C: viral protein 3
D: viral protein 4
H: EV68-159 heavy chain


Theoretical massNumber of molelcules
Total (without water)119,6576
Polymers119,6576
Non-polymers00
Water0
1
L: EV68-159 light chain
A: viral protein 1
B: viral protein 2
C: viral protein 3
D: viral protein 4
H: EV68-159 heavy chain
x 60


Theoretical massNumber of molelcules
Total (without water)7,179,401360
Polymers7,179,401360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
L: EV68-159 light chain
A: viral protein 1
B: viral protein 2
C: viral protein 3
D: viral protein 4
H: EV68-159 heavy chain
x 5


  • icosahedral pentamer
  • 598 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)598,28330
Polymers598,28330
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
L: EV68-159 light chain
A: viral protein 1
B: viral protein 2
C: viral protein 3
D: viral protein 4
H: EV68-159 heavy chain
x 6


  • icosahedral 23 hexamer
  • 718 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)717,94036
Polymers717,94036
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Viral protein ... , 4 types, 4 molecules ABCD

#2: Protein viral protein 1 / / VP1


Mass: 32920.309 Da / Num. of mol.: 1 / Fragment: UNP residues 565-861
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus D68 / Strain: US/MO/14-18047 / Cell (production host): spindle / Cell line (production host): RD / Production host: Homo sapiens (human) / Tissue (production host): muscle / References: UniProt: A0A097BW12
#3: Protein viral protein 2 / / VP2


Mass: 27567.135 Da / Num. of mol.: 1 / Fragment: UNP residues 70-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus D68 / Strain: US/MO/14-18047 / Cell (production host): spindle / Cell line (production host): RD / Production host: Homo sapiens (human) / Tissue (production host): muscle / References: UniProt: A0A0A7X639, UniProt: A0A097BW12*PLUS
#4: Protein viral protein 3 / / VP3


Mass: 27112.814 Da / Num. of mol.: 1 / Fragment: UNP residues 318-564
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus D68 / Strain: US/MO/14-18047 / Cell (production host): spindle / Cell line (production host): RD / Production host: Homo sapiens (human) / Tissue (production host): muscle / References: UniProt: A0A097BW12
#5: Protein viral protein 4 / / VP4


Mass: 7336.960 Da / Num. of mol.: 1 / Fragment: UNP residues 2-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus D68 / Strain: US/MO/14-18047 / Cell (production host): spindle / Cell line (production host): RD / Production host: Homo sapiens (human) / Tissue (production host): muscle / References: UniProt: A0A126D252, UniProt: J9Z449*PLUS

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Antibody , 2 types, 2 molecules LH

#1: Antibody EV68-159 light chain


Mass: 11715.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#6: Antibody EV68-159 heavy chain


Mass: 13003.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Enterovirus D68 in complex with human monoclonal antibody EV68-159Enterovirus 68COMPLEXall0MULTIPLE SOURCES
2Enterovirus D68Enterovirus 68VIRUS#2-#51RECOMBINANT
3human antibody EV68-159COMPLEX#1, #61RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
12Enterovirus D6842789US/MO/14-18947
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
12Homo sapiens (human)9606RD
23Cricetulus griseus (Chinese hamster)10029CHO
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in.
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12 sec. / Electron dose: 31.4 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 732
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameCategory
1FindEMparticle selection
2Leginonimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9jsprinitial Euler assignment
10jsprfinal Euler assignment
11RELIONclassification
12J3DR3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 42078
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30554 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 4WM8

4wm8

Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058149
ELECTRON MICROSCOPYf_angle_d0.65511098
ELECTRON MICROSCOPYf_dihedral_angle_d9.8394813
ELECTRON MICROSCOPYf_chiral_restr0.0481240
ELECTRON MICROSCOPYf_plane_restr0.0051432

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