+Open data
-Basic information
Entry | Database: PDB / ID: 3iyo | ||||||
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Title | Cryo-EM model of virion-sized HEV virion-sized capsid | ||||||
Components | Capsid protein | ||||||
Keywords | VIRUS / Amino Acid Sequence / Capsid / Capsid Proteins / Cryoelectron Microscopy / Dimerization / Image Processing / Computer-Assisted / Molecular Sequence Data / hepatitis E virus / Protein Conformation / Protein Folding / Protein Structure / Recombinant viral capsid / Virus Assembly / icosahedral virus | ||||||
Function / homology | Function and homology information viral capsid / host cell surface / host cell cytoplasm / structural molecule activity / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Hepatitis E virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.5 Å | ||||||
Authors | Xing, L. / Mayazaki, N. / Li, T.C. / Simons, M.N. / Wall, J.S. / Moore, M. / Wang, C.Y. / Takeda, N. / Wakita, T. / Miyamura, T. / Cheng, R.H. | ||||||
Citation | Journal: J Biol Chem / Year: 2010 Title: Structure of hepatitis E virion-sized particle reveals an RNA-dependent viral assembly pathway. Authors: Li Xing / Tian-Cheng Li / Naoyuki Mayazaki / Martha N Simon / Joseph S Wall / Mary Moore / Che-Yen Wang / Naokazu Takeda / Takaji Wakita / Tatsuo Miyamura / R Holland Cheng / Abstract: Hepatitis E virus (HEV) induces acute hepatitis in humans with a high fatality rate in pregnant women. There is a need for anti-HEV research to understand the assembly process of HEV native capsid. ...Hepatitis E virus (HEV) induces acute hepatitis in humans with a high fatality rate in pregnant women. There is a need for anti-HEV research to understand the assembly process of HEV native capsid. Here, we produced a large virion-sized and a small T=1 capsid by expressing the HEV capsid protein in insect cells with and without the N-terminal 111 residues, respectively, for comparative structural analysis. The virion-sized capsid demonstrates a T=3 icosahedral lattice and contains RNA fragment in contrast to the RNA-free T=1 capsid. However, both capsids shared common decameric organization. The in vitro assembly further demonstrated that HEV capsid protein had the intrinsic ability to form decameric intermediate. Our data suggest that RNA binding is the extrinsic factor essential for the assembly of HEV native capsids. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3iyo.cif.gz | 60.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iyo.ent.gz | 32.1 KB | Display | PDB format |
PDBx/mmJSON format | 3iyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3iyo_validation.pdf.gz | 977.5 KB | Display | wwPDB validaton report |
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Full document | 3iyo_full_validation.pdf.gz | 976.9 KB | Display | |
Data in XML | 3iyo_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 3iyo_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/3iyo ftp://data.pdbj.org/pub/pdb/validation_reports/iy/3iyo | HTTPS FTP |
-Related structure data
Related structure data | 5173MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 71031.766 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Hepatitis E virus / References: UniProt: Q1AHV0 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Hepatitis E capsid / Type: VIRUS | ||||||||||||
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Molecular weight |
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Details of virus | Empty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE | ||||||||||||
Natural host | Organism: Homo sapiens | ||||||||||||
Buffer solution | Name: MES-K buffer / pH: 6.2 / Details: 20mM MES-K | ||||||||||||
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 20mM MES-K | ||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 93 K |
-Electron microscopy imaging
Microscopy | Model: JEOL 2100F |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Cs: 2 mm / Camera length: 0 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: single-tilt / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 10 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: each micrograph | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: Polar Fourier Transform (PFT) / Resolution: 10.5 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 4348 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: cross-correlation Details: REFINEMENT PROTOCOL--Rigid Body DETAILS--Monomer C were divided into Shell and Spike domains and separately fitted by manual docking using program O and followed by Situs | ||||||||||||
Atomic model building | PDB-ID: 2ZZQ Pdb chain-ID: A / Accession code: 2ZZQ / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST
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