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- PDB-5apm: Multiple capsid-stabilizing protein-RNA and protein-protein inter... -

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Basic information

Entry
Database: PDB / ID: 5apm
TitleMultiple capsid-stabilizing protein-RNA and protein-protein interactions revealed in a high-resolution structure of an emerging picornavirus causing neonatal sepsis
Components
  • VP0
  • VP1
  • VP3
KeywordsVIRUS / PICORNAVIRUS / PARECHOVIRUS / HUMAN PARECHOVIRUS 3 / HPEV3 / NEONATAL SEPSIS / CRYOEM / IMAGE PROCESSING / SINGLE PARTICLE ANALYSIS
Function / homology
Function and homology information


RNA-protein covalent cross-linking / : / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / viral capsid / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell ...RNA-protein covalent cross-linking / : / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / viral capsid / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / virion attachment to host cell / RNA binding / ATP binding
Similarity search - Function
Viral polyprotein, parechovirus P3B / Parechovirus Genome-linked protein / Viral polyprotein, parechovirus P3A / Picornaviridae P3A protein / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid ...Viral polyprotein, parechovirus P3B / Parechovirus Genome-linked protein / Viral polyprotein, parechovirus P3A / Picornaviridae P3A protein / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / 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. / 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 PARECHOVIRUS 3
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 4.3 Å
AuthorsShakeel, S. / Westerhuis, B.M. / Domanska, A. / Koning, R.I. / Matadeen, R. / Koster, A.J. / Bakker, A.Q. / Beaumont, T. / Wolthers, K.C. / Butcher, S.J.
CitationJournal: Nat Commun / Year: 2016
Title: Multiple capsid-stabilizing interactions revealed in a high-resolution structure of an emerging picornavirus causing neonatal sepsis.
Authors: Shabih Shakeel / Brenda M Westerhuis / Ausra Domanska / Roman I Koning / Rishi Matadeen / Abraham J Koster / Arjen Q Bakker / Tim Beaumont / Katja C Wolthers / Sarah J Butcher /
Abstract: The poorly studied picornavirus, human parechovirus 3 (HPeV3) causes neonatal sepsis with no therapies available. Our 4.3-Å resolution structure of HPeV3 on its own and at 15 Å resolution in ...The poorly studied picornavirus, human parechovirus 3 (HPeV3) causes neonatal sepsis with no therapies available. Our 4.3-Å resolution structure of HPeV3 on its own and at 15 Å resolution in complex with human monoclonal antibody Fabs demonstrates the expected picornavirus capsid structure with three distinct features. First, 25% of the HPeV3 RNA genome in 60 sites is highly ordered as confirmed by asymmetric reconstruction, and interacts with conserved regions of the capsid proteins VP1 and VP3. Second, the VP0 N terminus stabilizes the capsid inner surface, in contrast to other picornaviruses where on expulsion as VP4, it forms an RNA translocation channel. Last, VP1's hydrophobic pocket, the binding site for the antipicornaviral drug, pleconaril, is blocked and thus inappropriate for antiviral development. Together, these results suggest a direction for development of neutralizing antibodies, antiviral drugs based on targeting the RNA-protein interactions and dissection of virus assembly on the basis of RNA nucleation.
History
DepositionSep 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.image_processing_id / _em_software.name
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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  • 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-3137
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  • Superimposition on EM map
  • EMDB-3137
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP1
B: VP3
C: VP0


Theoretical massNumber of molelcules
Total (without water)77,9993
Polymers77,9993
Non-polymers00
Water0
1
A: VP1
B: VP3
C: VP0
x 60


Theoretical massNumber of molelcules
Total (without water)4,679,969180
Polymers4,679,969180
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
A: VP1
B: VP3
C: VP0
x 5


  • icosahedral pentamer
  • 390 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)389,99715
Polymers389,99715
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1
B: VP3
C: VP0
x 6


  • icosahedral 23 hexamer
  • 468 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)467,99718
Polymers467,99718
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

#1: Protein VP1


Mass: 22393.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN PARECHOVIRUS 3 / Cell line: VERO / Variant: 152037 / References: UniProt: D2IE17
#2: Protein VP3


Mass: 26663.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN PARECHOVIRUS 3 / Cell line: VERO / Variant: 152037 / References: UniProt: D2IE17
#3: Protein VP0


Mass: 28943.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN PARECHOVIRUS 3 / Cell line: VERO / Variant: 152037 / References: UniProt: D2IE17
Sequence detailsWE MODELLED RESIDUES 24-221. WE MODELLED RESIDUES 20-256. WE MODELLED RESIDUES 20-282.

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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: HUMAN PARECHOVIRUS 3 / Type: VIRUS / Details: FORMALDEHYDE-INACTIVATED VIRUS WAS IMAGED.
Buffer solutionName: 10MM TRIS-HCL, 150MM NACL, 1MM MGCL2 / pH: 7.5 / Details: 10MM TRIS-HCL, 150MM NACL, 1MM MGCL2
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jan 21, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 2340 nm / Nominal defocus min: 420 nm / Cs: 0.01 mm
Image recordingElectron dose: 36 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 1028

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Processing

EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2ResMapother
3ETHANparticle selection
4Auto3DEM3D reconstruction
5EMAN13D reconstruction
6EMAN23D reconstruction
7RELION3D reconstruction
CTF correctionDetails: MICROGRAPHS
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: MAXIMUM LIKELIHOOD METHOD. / Resolution: 4.3 Å / Num. of particles: 8889 / Nominal pixel size: 1.14 Å
Details: WE DID NOT MODELLED DISORDERED REGIONS. THE PROVIDE COORDINATES ARE FOR AN ASYMMETRIC UNIT OF THE VIRUS. IN ORDER TO GENERATE THE WHOLE CAPSID, PLEASE USE THE MATRICES PROVIDED IN REMARK 350. ...Details: WE DID NOT MODELLED DISORDERED REGIONS. THE PROVIDE COORDINATES ARE FOR AN ASYMMETRIC UNIT OF THE VIRUS. IN ORDER TO GENERATE THE WHOLE CAPSID, PLEASE USE THE MATRICES PROVIDED IN REMARK 350. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3137. (DEPOSITION ID: 13643).
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--LOCAL CORRELATION REFINEMENT PROTOCOL--HOMOLOGY MODEL
RefinementHighest resolution: 4.3 Å
Refinement stepCycle: LAST / Highest resolution: 4.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 0 0 0 5490

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