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Yorodumi- EMDB-2550: Four levels of hierarchical organization including non-covalent c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2550 | |||||||||
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Title | Four levels of hierarchical organization including non-covalent chainmail brace the mature tumor herpesvirus capsid against pressurization | |||||||||
Map data | Capsid reconstruction of the rhesus monkey rhadinovirus | |||||||||
Sample |
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Keywords | gammaherpesvirus / virus / Rhesus monkey rhadinovirus / non-covalent chainmail | |||||||||
Biological species | Macaca mulatta rhadinovirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.2 Å | |||||||||
Authors | Zhou ZH / Hui W / Shah S / Jih J / O'Connor C / Sherman M / Kedes D / Schein S | |||||||||
Citation | Journal: Structure / Year: 2014 Title: Four levels of hierarchical organization, including noncovalent chainmail, brace the mature tumor herpesvirus capsid against pressurization. Authors: Z Hong Zhou / Wong Hoi Hui / Sanket Shah / Jonathan Jih / Christine M O'Connor / Michael B Sherman / Dean H Kedes / Stan Schein / Abstract: Like many double-stranded DNA viruses, tumor gammaherpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus withstand high internal pressure. Bacteriophage HK97 uses covalent ...Like many double-stranded DNA viruses, tumor gammaherpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus withstand high internal pressure. Bacteriophage HK97 uses covalent chainmail for this purpose, but how this is achieved noncovalently in the much larger gammaherpesvirus capsid is unknown. Our cryoelectron microscopy structure of a gammaherpesvirus capsid reveals a hierarchy of four levels of organization: (1) Within a hexon capsomer, each monomer of the major capsid protein (MCP), 1,378 amino acids and six domains, interacts with its neighboring MCPs at four sites. (2) Neighboring capsomers are linked in pairs by MCP dimerization domains and in groups of three by heterotrimeric triplex proteins. (3) Small (∼280 amino acids) HK97-like domains in MCP monomers alternate with triplex heterotrimers to form a belt that encircles each capsomer. (4) One hundred sixty-two belts concatenate to form noncovalent chainmail. The triplex heterotrimer orchestrates all four levels and likely drives maturation to an angular capsid that can withstand pressurization. | |||||||||
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_2550.map.gz | 728.9 MB | EMDB map data format | |
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Header (meta data) | emd-2550-v30.xml emd-2550.xml | 10.5 KB 10.5 KB | Display Display | EMDB header |
Images | emd_2550.jpg | 212.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2550 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2550 | HTTPS FTP |
-Validation report
Summary document | emd_2550_validation.pdf.gz | 221 KB | Display | EMDB validaton report |
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Full document | emd_2550_full_validation.pdf.gz | 220.1 KB | Display | |
Data in XML | emd_2550_validation.xml.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2550 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2550 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2550.map.gz / Format: CCP4 / Size: 953.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Capsid reconstruction of the rhesus monkey rhadinovirus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.04 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 : Rhesus monkey rhadinovirus capsid
Entire | Name: Rhesus monkey rhadinovirus capsid |
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Components |
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-Supramolecule #1000: Rhesus monkey rhadinovirus capsid
Supramolecule | Name: Rhesus monkey rhadinovirus capsid / type: sample / ID: 1000 / Details: The capsid has T=16 icosahedral symmetry. / Oligomeric state: icosahedral viral capsid / Number unique components: 1 |
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Molecular weight | Theoretical: 198.4 MDa / Method: theoreomatic estimation |
-Supramolecule #1: Macaca mulatta rhadinovirus
Supramolecule | Name: Macaca mulatta rhadinovirus / type: virus / ID: 1 / NCBI-ID: 703611 / Sci species name: Macaca mulatta rhadinovirus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Macaca mulatta (Rhesus monkey) / synonym: VERTEBRATES |
Molecular weight | Experimental: 198.4 MDa / Theoretical: 198.4 MDa |
Virus shell | Shell ID: 1 / Name: capsid / Diameter: 1300 Å / T number (triangulation number): 16 |
-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: 8 / Details: 20mM Tris HCl at pH 8.0, 250 mM NaCl and 1 mM EDTA |
Grid | Details: Quantifoil R2/1 grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 40 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Method: Blot manually for about 1 second before plunging. |
-Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/T |
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Temperature | Min: 80 K / Max: 100 K / Average: 90 K |
Date | Aug 30, 2004 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 320 / Average electron dose: 10 e/Å2 / Bits/pixel: 14 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 33000 |
Sample stage | Specimen holder: 626 / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Details | Data processing and 3D reconstruction were carried out in Microsoft Windows XP-based HP workstations with the IMIRS package |
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CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: OTHER / Software - Name: IMIRS / Number images used: 14374 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: fit in map function from Chimera |