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- PDB-5apm: Multiple capsid-stabilizing protein-RNA and protein-protein inter... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5apm | ||||||
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Title | Multiple capsid-stabilizing protein-RNA and protein-protein interactions revealed in a high-resolution structure of an emerging picornavirus causing neonatal sepsis | ||||||
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![]() | VIRUS / PICORNAVIRUS / PARECHOVIRUS / HUMAN PARECHOVIRUS 3 / HPEV3 / NEONATAL SEPSIS / CRYOEM / IMAGE PROCESSING / SINGLE PARTICLE ANALYSIS | ||||||
Function / homology | ![]() 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 / virion attachment to host cell / structural molecule activity / RNA binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / Resolution: 4.3 Å | ||||||
![]() | Shakeel, 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. | ||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.5 KB | Display | ![]() |
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PDB format | ![]() | 100.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 970 KB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 50 KB | Display | |
Data in CIF | ![]() | 71.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3137MC ![]() 3138C ![]() 3322C M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 3.3 TB Data #1: Selected aligned movie frames, aligned-averaged micrographs and particle coordinates of human parechovirus 3 (HPeV3) virions [Aligned movie frames (.mrcs extension), aligned-averaged ...Data #1: Selected aligned movie frames, aligned-averaged micrographs and particle coordinates of human parechovirus 3 (HPeV3) virions [Aligned movie frames (.mrcs extension), aligned-averaged micrographs (.mrc extension) and particle coordinates (.box extension)] Data #2: Unaligned movie frames of human parechovirus 3 (HPeV3) virions [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
#1: Protein | Mass: 22393.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 26663.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 28943.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
Sequence details | WE MODELLED RESIDUES 24-221. WE MODELLED RESIDUES 20-256. WE MODELLED RESIDUES 20-282. |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: HUMAN PARECHOVIRUS 3 / Type: VIRUS / Details: FORMALDEHYDE-INACTIVATED VIRUS WAS IMAGED. |
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Buffer solution | Name: 10MM TRIS-HCL, 150MM NACL, 1MM MGCL2 / pH: 7.5 / Details: 10MM TRIS-HCL, 150MM NACL, 1MM MGCL2 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: 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 |
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Microscopy | Model: FEI TITAN KRIOS / Date: Jan 21, 2015 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 2340 nm / Nominal defocus min: 420 nm / Cs: 0.01 mm |
Image recording | Electron dose: 36 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Num. digital images: 1028 |
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Processing
EM software |
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CTF correction | Details: MICROGRAPHS | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||
3D reconstruction | Method: 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 building | Protocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient Details: METHOD--LOCAL CORRELATION REFINEMENT PROTOCOL--HOMOLOGY MODEL | ||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 4.3 Å | ||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 4.3 Å
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