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- PDB-8x9b: Cryo-EM structure of coxsackievirus A16 empty particle in complex... -

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Basic information

Entry
Database: PDB / ID: 8x9b
TitleCryo-EM structure of coxsackievirus A16 empty particle in complex with Fab h1A6.2 (local refinement)
Components
  • (Genome polyprotein) x 2
  • Capsid protein VP1
  • The heavy chain of Fab h1A6.2
  • The light chain of Fab h1A6.2
KeywordsVIRAL PROTEIN / Cryo-EM / virus / coxsackievirus A16
Function / homology
Function and homology information


symbiont genome entry into host cell via pore formation in plasma membrane / symbiont-mediated suppression of host gene expression / viral capsid / virion attachment to host cell / structural molecule activity
Similarity search - Function
Picornavirus coat protein / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Coxsackievirus A16
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.82 Å
AuthorsJiang, Y. / Huang, Y. / Zhu, R. / Zheng, Q. / Li, S. / Xia, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of coxsackievirus A16 empty particle in complex with Fab h1A6.2 (local refinement)
Authors: Jiang, Y. / Huang, Y. / Zhu, R. / Zheng, Q. / Li, S. / Xia, N.
History
DepositionNov 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Capsid protein VP1
E: Capsid protein VP1
G: Genome polyprotein
I: Genome polyprotein
K: Genome polyprotein
M: Genome polyprotein
O: The heavy chain of Fab h1A6.2
P: The light chain of Fab h1A6.2
F: Capsid protein VP1
H: Capsid protein VP1
J: Genome polyprotein
L: Genome polyprotein
N: Genome polyprotein
Q: Genome polyprotein
R: The heavy chain of Fab h1A6.2
S: The light chain of Fab h1A6.2


Theoretical massNumber of molelcules
Total (without water)399,09716
Polymers399,09716
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Capsid protein VP1


Mass: 33106.352 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A16 / References: UniProt: A0A2S1BJ89
#2: Protein
Genome polyprotein


Mass: 27557.104 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A16 / References: UniProt: A0A2S1BJ89
#3: Protein
Genome polyprotein


Mass: 26654.295 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A16 / References: UniProt: A0A2S1BJ89
#4: Antibody The heavy chain of Fab h1A6.2


Mass: 12563.226 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#5: Antibody The light chain of Fab h1A6.2


Mass: 12349.966 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
Has protein modificationY

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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
1Coxsackievirus A16 empty particle in complex with Fab h1A6.2COMPLEXall0MULTIPLE SOURCES
2Coxsackievirus A16 empty particleVIRUS#1-#31NATURAL
3The Fab of h1A6.2COMPLEX#4-#51RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Coxsackievirus A1631704
23Mus musculus (house mouse)10090
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: YES / Enveloped: NO / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125196 / Symmetry type: POINT

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