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Yorodumi- EMDB-5173: Cryo-EM structure of virion-sized hepatitis E virus-like particle -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5173 | |||||||||
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Title | Cryo-EM structure of virion-sized hepatitis E virus-like particle | |||||||||
Map data | This is a map for the virion-sized hepatitis E virus-like particle | |||||||||
Sample |
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Keywords | assembly pathway | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 10.5 Å | |||||||||
Authors | Xing L / Mayazaki N / Li TC / Simons MN / Wall JS / Moore M / Wang CY / Takeda N / Wakita T / Miyamura T / Cheng RH | |||||||||
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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5173.map.gz | 49.5 MB | EMDB map data format | |
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Header (meta data) | emd-5173-v30.xml emd-5173.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | emd_5173_1.png | 312.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5173 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5173 | HTTPS FTP |
-Validation report
Summary document | emd_5173_validation.pdf.gz | 407.7 KB | Display | EMDB validaton report |
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Full document | emd_5173_full_validation.pdf.gz | 407.3 KB | Display | |
Data in XML | emd_5173_validation.xml.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5173 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5173 | HTTPS FTP |
-Related structure data
Related structure data | 3iyoMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5173.map.gz / Format: CCP4 / Size: 118.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a map for the virion-sized hepatitis E virus-like particle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Hepatitis E virus like particle
Entire | Name: Hepatitis E virus like particle |
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Components |
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-Supramolecule #1000: Hepatitis E virus like particle
Supramolecule | Name: Hepatitis E virus like particle / type: sample / ID: 1000 / Oligomeric state: 1 / Number unique components: 2 |
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Molecular weight | Experimental: 11.8 MDa / Theoretical: 12.2 MDa / Method: STEM |
-Supramolecule #1: Hepatitis E virus
Supramolecule | Name: Hepatitis E virus / type: virus / ID: 1 / Name.synonym: recombinant virus-like particle / NCBI-ID: 12461 / Sci species name: Hepatitis E virus / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: recombinant virus-like particle |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Molecular weight | Experimental: 11.8 MDa / Theoretical: 12.2 MDa |
Virus shell | Shell ID: 1 / Name: ORF2 protein / Diameter: 410 Å / T number (triangulation number): 3 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 6.2 / Details: 20mM MES-K |
Grid | Details: 300 mesh holey carbon |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 93 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunger |
-Electron microscopy
Microscope | JEOL 2100F |
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Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 10 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 50000 |
Sample stage | Specimen holder: single-tilt / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: each micrograph |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: P3DR / Number images used: 4348 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Situs |
Details | PDBEntryID_givenInChain. Protocol: Rigid Body. Monomer C were divided into Shell and Spike domains and separately fitted by manual docking using program O and followed by Situs |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation |
Output model | PDB-3iyo: |