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Yorodumi- EMDB-2435: Protein Interactions in the Murine Cytomegalovirus Capsid Reveale... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2435 | |||||||||
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Title | Protein Interactions in the Murine Cytomegalovirus Capsid Revealed by CryoEM | |||||||||
Map data | Reconstruction of Murine Cytomegalovirus | |||||||||
Sample |
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Keywords | cytomegalovirus / herpes simplex virus type 1 / electron cryo microscopy / three-dimensional / major capsid protein. | |||||||||
Biological species | Murid herpesvirus 1 (Murine cytomegalovirus) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 9.1 Å | |||||||||
Authors | Hui W / Tang Q / Liu H / Atanasov I / Zhu H / Zhou ZH | |||||||||
Citation | Journal: Protein Cell / Year: 2013 Title: Protein interactions in the murine cytomegalovirus capsid revealed by cryoEM. Authors: Wong H Hui / Qiyi Tang / Hongrong Liu / Ivo Atanasov / Fenyong Liu / Hua Zhu / Z Hong Zhou / Abstract: Cytomegalovirus (CMV) is distinct among members of the Herpesviridae family for having the largest dsDNA genome (230 kb). Packaging of large dsDNA genome is known to give rise to a highly pressurized ...Cytomegalovirus (CMV) is distinct among members of the Herpesviridae family for having the largest dsDNA genome (230 kb). Packaging of large dsDNA genome is known to give rise to a highly pressurized viral capsid, but molecular interactions conducive to the formation of CMV capsid resistant to pressurization have not been described. Here, we report a cryo electron microscopy (cryoEM) structure of the murine cytomegalovirus (MCMV) capsid at a 9.1 Å resolution and describe the molecular interactions among the ∼3000 protein molecules in the MCMV capsid at the secondary structure level. Secondary structural elements are resolved to provide landmarks for correlating with results from sequence-based prediction and for structure-based homology modeling. The major capsid protein (MCP) upper domain (MCPud) contains α-helices and β-sheets conserved with those in MCPud of herpes simplex virus type 1 (HSV-1), with the largest differences identified as a "saddle loop" region, located at the tip of MCPud and involved in interaction with the smallest capsid protein (SCP). Interactions among the bacteriophage HK97-like floor domain of MCP, the middle domain of MCP, the hook and clamp domains of the triplex proteins (hoop and clamp domains of TRI-1 and clamp domain of TRI-2) contribute to the formation of a mature capsid. These results offer a framework for understanding how cytomegalovirus uses various secondary structural elements of its capsid proteins to build a robust capsid for packaging its large dsDNA genome inside and for attaching unique functional tegument proteins outside. | |||||||||
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_2435.map.gz | 754.6 MB | EMDB map data format | |
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Header (meta data) | emd-2435-v30.xml emd-2435.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_2435.png | 495.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2435 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2435 | HTTPS FTP |
-Validation report
Summary document | emd_2435_validation.pdf.gz | 236.1 KB | Display | EMDB validaton report |
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Full document | emd_2435_full_validation.pdf.gz | 235.2 KB | Display | |
Data in XML | emd_2435_validation.xml.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2435 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2435 | 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_2435.map.gz / Format: CCP4 / Size: 817.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Murine Cytomegalovirus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.8 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 : Murine cytomegalovirus capsid
Entire | Name: Murine cytomegalovirus capsid |
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Components |
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-Supramolecule #1000: Murine cytomegalovirus capsid
Supramolecule | Name: Murine cytomegalovirus capsid / type: sample / ID: 1000 / Details: The sample is monodisperse in PBS buffer / Oligomeric state: icosahedral virus capsid / Number unique components: 4 |
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Molecular weight | Theoretical: 186.4 MDa |
-Supramolecule #1: Murid herpesvirus 1
Supramolecule | Name: Murid herpesvirus 1 / type: virus / ID: 1 / Name.synonym: Murine cytomegalovirus Details: The virus is enveloped but the structure presented here is for the capsid only. NCBI-ID: 10366 / Sci species name: Murid herpesvirus 1 / Sci species strain: strain Smith / Virus type: OTHER / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes / Syn species name: Murine cytomegalovirus |
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Host (natural) | Organism: Murine / Strain: strain Smith / synonym: INVERTEBRATES |
Molecular weight | Theoretical: 186.4 MDa |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 1310 Å / T number (triangulation number): 16 |
-Experimental details
-Structure determination
Method | negative staining, 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: 7 / Details: PBS |
Staining | Type: NEGATIVE / Details: vitreous ice, no staining |
Grid | Details: across holes in Quantifoil grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK I / Details: Vitrification instrument: FEI Vitrobot / Method: Blot for 7-9 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80 K / Max: 100 K / Average: 90 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 250,000 times magnification Legacy - Electron beam tilt params: 0 |
Specialist optics | Energy filter - Name: FEI |
Date | Oct 15, 2009 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 1299 / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder: Autoloader of Titan Krios at liquid nitrogen temperature Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Individual particle images were automatically boxed out from micrographs by the autoBox program in the IMIRS package, followed by manual screening to select good capsid particle images that appear perfectly intact and without contamination and signs of specimen charging. Defocus value and astigmatism parameters of each micrographs were determined with CTFFIND. Subsequent data processing includes the determination of particle orientation/center parameters, 3D reconstruction and iterative, projection-based refinement by a distributed computing approach using modular programs in the IMIRS package with recent enhancements. The distributed computing was performed entirely through on six Microsoft Windows personal computers and four Windows servers within a custom-designed MPI network. Astigmatism was taken into consideration during the correction of contrast transfer function (CTF) both in the orientation/center refinement step and the 3D reconstruction step. Using this procedure, we first obtained a 3D map from 6402 particle images from the Polara micrographs. This map has a resolution of about 11 angstrom and was used as the starting model to assist processing the higher resolution particle images of the Titan micrographs. To process the Titan micrographs, we discarded micrographs with specimen charging by evaluating the Fourier transform of the micrographs and selected 669 micrographs for in-depth data processing. From the 669 good Titan micrographs selected out through this process, we boxed 5383 particle images and determined their orientation/center parameters by using the 11 angstrom map as the starting model. These orientation/center parameters were iteratively refined against the latest 3D map by gradually including Fourier data at regions of higher spatial frequency. The iterative process was terminated when the reconstruction converges to a stable solution and no further improvement in the resolution of the map was observed. Our reconstruction converges when the high spatial frequency cut-off of the included image data reached 1/6.9 angstrom-1. The final map was obtained from 3467 particles images, all from the Titan micrographs. |
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CTF correction | Details: CTFFIND |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMIRS / Number images used: 3467 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera |
Details | Manual fitting in Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Chimera fit-to-map |