[English] 日本語
Yorodumi- EMDB-8248: Subtomogram-averaged surface glycoprotein spike density of rubell... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8248 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Subtomogram-averaged surface glycoprotein spike density of rubella virus | |||||||||
Map data | Sub-tomogram averaged surface glycoprotein spike density of rubella virus | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding ...T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Rubella virus | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 11.1 Å | |||||||||
Authors | Mangala Prasad V / Klose T / Rossmann MG | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: PLoS Pathog / Year: 2017 Title: Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus. Authors: Vidya Mangala Prasad / Thomas Klose / Michael G Rossmann / Abstract: Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe ...Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8248.map.gz | 553.3 KB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-8248-v30.xml emd-8248.xml | 13.5 KB 13.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8248_fsc.xml | 5.4 KB | Display | FSC data file |
Images | emd_8248.png | 82.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8248 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8248 | HTTPS FTP |
-Validation report
Summary document | emd_8248_validation.pdf.gz | 330.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_8248_full_validation.pdf.gz | 330 KB | Display | |
Data in XML | emd_8248_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | emd_8248_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8248 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8248 | HTTPS FTP |
-Related structure data
Related structure data | 5khcMC 8249C 8250C 8251C 5kheC 5khfC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_8248.map.gz / Format: CCP4 / Size: 605.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sub-tomogram averaged surface glycoprotein spike density of rubella virus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.64 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Rubella virus E1-E2 glycoprotein spike
Entire | Name: Rubella virus E1-E2 glycoprotein spike |
---|---|
Components |
|
-Supramolecule #1: Rubella virus E1-E2 glycoprotein spike
Supramolecule | Name: Rubella virus E1-E2 glycoprotein spike / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Molecular weight | Theoretical: 85 KDa |
-Macromolecule #1: E1 glycoprotein
Macromolecule | Name: E1 glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Rubella virus |
Molecular weight | Theoretical: 50.573352 KDa |
Recombinant expression | Organism: Cercopithecus aethiops (grivet) |
Sequence | String: EEAFTYLCTA PGCATQTPVP VRLAGVRFES KIVDGGCFAP WDLEATGACI CEIPTDVSCE GLGAWVPTAP CARIWNGTQR ACTFWAVNA YSSGGYAQLA SYFNPGGSYY KQYHPTACEV EPAFGHSDAA CWGFPTDTVM SVFALASYVQ HPHKTVRVKF H TETRTVWQ ...String: EEAFTYLCTA PGCATQTPVP VRLAGVRFES KIVDGGCFAP WDLEATGACI CEIPTDVSCE GLGAWVPTAP CARIWNGTQR ACTFWAVNA YSSGGYAQLA SYFNPGGSYY KQYHPTACEV EPAFGHSDAA CWGFPTDTVM SVFALASYVQ HPHKTVRVKF H TETRTVWQ LSVAGVSCNV TTEHPFCNTP HGQLEVQVPP DPGDLVEYIM NYTGNQQSRW GLGSPNCHGP DWASPVCQRH SP DCSRLVG ATPERPRLRL VDADDPLLRT APGPGEVWVT PVIGSQARKC GLHIRAGPYG HATVEMPEWI HAHTTSDPWH PPG PLGLKF KTVRPVALPR ALAPPRNVRV TGCYQCGTPA LVEGLAPGGG NCHLTVNGED VGAFPPGKFV TAALLNTPPP YQVS CGGES DRASARVIDP AAQSFTGVVY GTHTTAVSET RFEDDDDKAG WSHPQFEKGG GSGGGSGGGS WSHPQFEK |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON | ||||||||||||
Vitrification | Cryogen name: ETHANE | ||||||||||||
Details | Rubella virus was purified from Vero cells. Glycoprotein spike volumes were extracted from the surface of virus tomograms. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 90.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 11000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |