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- PDB-9pi8: EV-D68 in complex with G12 Fc -

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Basic information

Entry
Database: PDB / ID: 9pi8
TitleEV-D68 in complex with G12 Fc
Components
  • G12 Fc fusion
  • viral protein 1
  • viral protein 2
  • viral protein 3
  • viral protein 4
KeywordsVIRUS/IMMUNE SYSTEM / EV-D68 / G12 / antibody / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / VIRUS / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell membrane / cysteine-type peptidase activity / helicase 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 / viral capsid ...host cell membrane / cysteine-type peptidase activity / helicase 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 / viral capsid / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / host cell cytoplasm / RNA helicase activity / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / 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 / proteolysis / RNA binding / zinc ion binding / ATP 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 / 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 / Genome polyprotein
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
enterovirus D68
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.11 Å
AuthorsKlose, T. / Kuhn, R.J. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN75N9302200035 United States
CitationJournal: Mol Ther / Year: 2026
Title: An RNA-to-RNA pipeline for rapid antiviral antibody development.
Authors: Edgar A Hodge / Jacob Archer / Jacqueline S Anderson / Nikole L Warner / Jacque Tremblay / Thomas Klose / Stephanie Park / Troy Hinkley / Amit P Khandhar / Richard Kuhn / Charles B Shoemaker / Jesse H Erasmus /
Abstract: Rapid development of antibody therapeutics is often hindered by dependencies on recombinant protein production, both for antigen generation and for antibody manufacturing. To overcome these ...Rapid development of antibody therapeutics is often hindered by dependencies on recombinant protein production, both for antigen generation and for antibody manufacturing. To overcome these bottlenecks, we established a self-amplifying replicon RNA (repRNA) immunization and therapeutic delivery platform that enables an end-to-end RNA-to-antibody-to-RNA workflow. In this approach, alpacas are immunized with repRNA encoding virus-like particles to elicit antibody responses, peripheral blood mononuclear cells are harvested to construct phage display libraries, and broadly neutralizing heavy-chain-only antibodies (VHHs [variable heavy domain of the heavy chain]) are identified through high-throughput screening. Lead VHHs are then re-encoded into repRNA for in vivo delivery as therapeutic constructs, with engineering options for valency, potency, and serum half-life. As proof of concept, we applied this platform against enterovirus D68 (EV-D68), an emerging pathogen associated with severe respiratory disease and acute flaccid myelitis in children for which no vaccines or treatments exist. repRNA-encoded VHHs protected mice from EV-D68 challenge in both lungs and nasal cavities, and cryoelectron microscopy revealed the capsid-binding footprint and mechanism of neutralization. Together, these findings demonstrate a modular platform for rapid discovery and delivery of antiviral biologics, with EV-D68 serving as a prototype application.
History
DepositionJul 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: viral protein 1
B: viral protein 2
C: viral protein 3
D: viral protein 4
E: G12 Fc fusion


Theoretical massNumber of molelcules
Total (without water)136,7635
Polymers136,7635
Non-polymers00
Water00
1
A: viral protein 1
B: viral protein 2
C: viral protein 3
D: viral protein 4
E: G12 Fc fusion
x 60


Theoretical massNumber of molelcules
Total (without water)8,205,794300
Polymers8,205,794300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: viral protein 1
B: viral protein 2
C: viral protein 3
D: viral protein 4
E: G12 Fc fusion
x 5


  • icosahedral pentamer
  • 684 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)683,81625
Polymers683,81625
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: viral protein 1
B: viral protein 2
C: viral protein 3
D: viral protein 4
E: G12 Fc fusion
x 6


  • icosahedral 23 hexamer
  • 821 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)820,57930
Polymers820,57930
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
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

#1: Protein viral protein 1


Mass: 34242.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) enterovirus D68
References: UniProt: A0A097BW12, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein viral protein 2 / VP2


Mass: 27567.135 Da / Num. of mol.: 1 / Fragment: UNP residues 70-317 / Source method: isolated from a natural source / Source: (natural) enterovirus D68 / References: UniProt: A0A0A7X639
#3: Protein viral protein 3 / VP3


Mass: 27112.814 Da / Num. of mol.: 1 / Fragment: UNP residues 318-564 / Source method: isolated from a natural source / Source: (natural) enterovirus D68 / References: UniProt: A0A097BW12
#4: Protein viral protein 4 / VP4


Mass: 7336.960 Da / Num. of mol.: 1 / Fragment: UNP residues 2-69 / Source method: isolated from a natural source / Source: (natural) enterovirus D68 / References: UniProt: A0A097BW12
#5: Antibody G12 Fc fusion


Mass: 40503.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Homo sapiens (human)
Has protein modificationN

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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

ComponentName: EV-D68 in complex with G12 Fc / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: enterovirus D68 / Strain: US/MO/14-18949
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 36.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6000

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIX1.21.2_5419model refinement
14ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 140113
3D reconstructionResolution: 2.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103582 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 31.59 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01067368
ELECTRON MICROSCOPYf_angle_d0.81610042
ELECTRON MICROSCOPYf_chiral_restr0.06061128
ELECTRON MICROSCOPYf_plane_restr0.00751305
ELECTRON MICROSCOPYf_dihedral_angle_d12.51422644

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