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- PDB-3j2j: Empty coxsackievirus A9 capsid -

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Basic information

Entry
Database: PDB / ID: 3j2j
TitleEmpty coxsackievirus A9 capsid
Components
  • Protein VP1
  • Protein VP2
  • Protein VP3
KeywordsVIRUS / CVA9-integrin / picornavirus / enterovirus / empty capsid
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / DNA replication / induction by virus of host autophagy / 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 / host cell nucleus / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
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
Biological speciesHuman coxsackievirus A9
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.54 Å
AuthorsShakeel, S. / Seitsonen, J.J.T. / Kajander, T. / Laurinmaki, P. / Hyypia, T. / Susi, P. / Butcher, S.J.
CitationJournal: J Virol / Year: 2013
Title: Structural and functional analysis of coxsackievirus A9 integrin αvβ6 binding and uncoating.
Authors: Shabih Shakeel / Jani J T Seitsonen / Tommi Kajander / Pasi Laurinmäki / Timo Hyypiä / Petri Susi / Sarah J Butcher /
Abstract: Coxsackievirus A9 (CVA9) is an important pathogen of the Picornaviridae family. It utilizes cellular receptors from the integrin αv family for binding to its host cells prior to entry and genome ...Coxsackievirus A9 (CVA9) is an important pathogen of the Picornaviridae family. It utilizes cellular receptors from the integrin αv family for binding to its host cells prior to entry and genome release. Among the integrins tested, it has the highest affinity for αvβ6, which recognizes the arginine-glycine-aspartic acid (RGD) loop present on the C terminus of viral capsid protein, VP1. As the atomic model of CVA9 lacks the RGD loop, we used surface plasmon resonance, electron cryo-microscopy, and image reconstruction to characterize the capsid-integrin interactions and the conformational changes on genome release. We show that the integrin binds to the capsid with nanomolar affinity and that the binding of integrin to the virion does not induce uncoating, thereby implying that further steps are required for release of the genome. Electron cryo-tomography and single-particle image reconstruction revealed variation in the number and conformation of the integrins bound to the capsid, with the integrin footprint mapping close to the predicted site for the exposed RGD loop on VP1. Comparison of empty and RNA-filled capsid reconstructions showed that the capsid undergoes conformational changes when the genome is released, so that the RNA-capsid interactions in the N termini of VP1 and VP4 are lost, VP4 is removed, and the capsid becomes more porous, as has been reported for poliovirus 1, human rhinovirus 2, enterovirus 71, and coxsackievirus A7. These results are important for understanding the structural basis of integrin binding to CVA9 and the molecular events leading to CVA9 cell entry and uncoating.
History
DepositionOct 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

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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
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  • Superimposition on EM map
  • EMDB-5514
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Protein VP1
B: Protein VP3
C: Protein VP2


Theoretical massNumber of molelcules
Total (without water)79,7973
Polymers79,7973
Non-polymers00
Water0
1
A: Protein VP1
B: Protein VP3
C: Protein VP2
x 60


Theoretical massNumber of molelcules
Total (without water)4,787,793180
Polymers4,787,793180
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: Protein VP1
B: Protein VP3
C: Protein VP2
x 5


  • icosahedral pentamer
  • 399 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)398,98315
Polymers398,98315
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Protein VP1
B: Protein VP3
C: Protein VP2
x 6


  • icosahedral 23 hexamer
  • 479 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)478,77918
Polymers478,77918
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Protein VP1 / P1D / Virion protein 1


Mass: 25541.980 Da / Num. of mol.: 1 / Fragment: UNP residues 631-852 / Source method: isolated from a natural source / Source: (natural) Human coxsackievirus A9 / References: UniProt: P21404
#2: Protein Protein VP3 / P1C / Virion protein 3


Mass: 26335.072 Da / Num. of mol.: 1 / Fragment: UNP residues 331-568 / Source method: isolated from a natural source / Source: (natural) Human coxsackievirus A9 / References: UniProt: P21404
#3: Protein Protein VP2 / P1B / Virion protein 2


Mass: 27919.494 Da / Num. of mol.: 1 / Fragment: UNP residues 79-330 / Source method: isolated from a natural source / Source: (natural) Human coxsackievirus A9 / References: UniProt: P21404

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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: Empty coxsackievirus A9 capsid in complex with integrin alpha v beta 6
Type: COMPLEX / Synonym: CVA9
Details of virusEmpty: YES / Enveloped: NO / Host category: VERTEBRATES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Homo sapiens
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE
Details: manual plunging into liquid ethane (GATAN CRYOPLUNGE 3)
Method: manual plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Feb 1, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 62000 X / Calibrated magnification: 62000 X / Nominal defocus max: 4120 nm / Nominal defocus min: 830 nm / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: GATAN 626 / Tilt angle max: 0 ° / Tilt angle min: 0 °
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1iMODFITmodel fitting
2Auto3DEM3D reconstruction
CTF correctionDetails: whole micrograph
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: polar Fourier transform / Resolution: 9.54 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 1200 / Nominal pixel size: 2.26 Å / Actual pixel size: 2.26 Å / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: REFINEMENT PROTOCOL--flexible fitting
Atomic model building

3D fitting-ID: 1 / Accession code: 1D4M / Initial refinement model-ID: 1 / PDB-ID: 1D4M

/ Source name: PDB / Type: experimental model

IDPdb chain-ID
1A
2B
3C
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms5601 0 0 0 5601

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