+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6712 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Inner capsid of Rice Dwarf Virus | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Biological species | Rice dwarf virus (isolate O) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.43 Å | |||||||||
Authors | Nakamichi Y / Miyazaki N / Tsutsumi K / Higashiura A / Murata K / Nakagawa A | |||||||||
Citation | Journal: Structure / Year: 2019 Title: An Assembly Intermediate Structure of Rice Dwarf Virus Reveals a Hierarchical Outer Capsid Shell Assembly Mechanism. Authors: Yusuke Nakamichi / Naoyuki Miyazaki / Kenta Tsutsumi / Akifumi Higashiura / Hirotaka Narita / Kazuyoshi Murata / Atsushi Nakagawa / Abstract: Nearly all viruses of the Reoviridae family possess a multi-layered capsid consisting of an inner layer with icosahedral T = 1 symmetry and a second-outer layer (composed of 260 copies of a trimeric ...Nearly all viruses of the Reoviridae family possess a multi-layered capsid consisting of an inner layer with icosahedral T = 1 symmetry and a second-outer layer (composed of 260 copies of a trimeric protein) exhibiting icosahedral T = 13 symmetry. Here we describe the construction and structural evaluation of an assembly intermediate of the Rice dwarf virus of the family Reoviridae stalled at the second capsid layer via targeted disruption of the trimer-trimer interaction interface in the second-layer capsid protein. Structural determination was performed by conventional and Zernike/Volta phase-contrast cryoelectron microscopy. The assembly defect second-layer capsid trimers bound exclusively to the outer surface of the innermost capsid layer at the icosahedral 3-fold axis. Furthermore, the second-layer assembly could not proceed without specific inter-trimer interactions. Our results suggest that the correct assembly pathway for second-layer capsid formation is highly controlled at the inter-layer and inter-trimer interactions. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6712.map.gz | 60.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6712-v30.xml emd-6712.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
Images | emd_6712.png | 65 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6712 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6712 | HTTPS FTP |
-Validation report
Summary document | emd_6712_validation.pdf.gz | 78.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_6712_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_6712_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6712 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6712 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_6712.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.88 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Rice dwarf virus (isolate O)
Entire | Name: Rice dwarf virus (isolate O) |
---|---|
Components |
|
-Supramolecule #1: Rice dwarf virus (isolate O)
Supramolecule | Name: Rice dwarf virus (isolate O) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 142805 / Sci species name: Rice dwarf virus (isolate O) / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
---|---|
Virus shell | Shell ID: 1 / Name: inner shell capsid / T number (triangulation number): 1 |
-Macromolecule #1: Core protein P3
Macromolecule | Name: Core protein P3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Rice dwarf virus (isolate O) |
Sequence | String: MDSTGRAYDG ASEFKSVLVT EGTSHYTPVE VYNILDELKT IKITSTIAEQ SVVSRTPIPL SKIGLQDVKK LFDINVIKCG SSLRIVDEPQ VTFIVSYAKD IYDKFMCIEH DSAYEPSLTM HRVRVIYSML NDYCAKMISE VPYESSFVGE LPVKSVTLNK LGDRNMDALA ...String: MDSTGRAYDG ASEFKSVLVT EGTSHYTPVE VYNILDELKT IKITSTIAEQ SVVSRTPIPL SKIGLQDVKK LFDINVIKCG SSLRIVDEPQ VTFIVSYAKD IYDKFMCIEH DSAYEPSLTM HRVRVIYSML NDYCAKMISE VPYESSFVGE LPVKSVTLNK LGDRNMDALA EHLLFEHDVV NAQRENRIFY QRKSAPAVPV IFGDDLEPAV RERANLYHRY SVPYHQIELA LHALANDLLS IQYCHPTVVY NYLSSRAPNF LRLDDQVSLK LTSAGIGTLM PRPVVQLLDY DLVYMSPLAL NNLASRLLRK ISLHLVMQMV TAVQQDLGEV VSVSSNVTNP ASACLVRMNV QGVQTLAVFI AQSMLNPNIS YGMISGLTLD CFSNFIYGAC LMLFQALIPP SALTARQRLD INNRFAYFLI KCHATQATTA RLVANQVIYP VDAIDQWQSN GRDVLVAIYN NLLPGELVLT NLIQTYFRGN TAQQAAEILI PADQTSYGAN ETRALSAPYL FGAPINMLAP DARLSTYKRD LALPDRSPIL ITTVEGQNSI SIENLRHKTG LIRAMYLNGF VTQPPAWIRN ANSNTALLSR FLDATPNLLG IYEAILANTY ANAVNVYCDS VYRADIPIEW KLHQSVDPQD LLFGVFGIVP QYQILNEAVP DFFAGGEDIL ILQLIRAVYD TLSNKLGRNP ADIFHLEEVF KVIEEIVSVL VQQKIDVRKY FTESMRSGSF SKPRWDNFLR RPVAQRLPNL YSVIMTQADH VYNYMTQLTH IIPITDCFYI VKNSGFVDRG STGPVIASSS VYENVLKVVH TIADFDAANA LRLQRRRVDN TSYTDSLSDM FNGLRSISSS EFVRSVNGRS VFTEGRIDAI KVNMRAKFDL QFITEEGGYS KPPNVKKLMF SDFLSFLDSH KSDYRPPLLT VPITIGLNNL GETNSNTLRM RSEAIDEYFS SYVGAQILVP INVVDTRVYT EFSELRNFFT GDVVIRDDPF DVWDGVKATY IPIGVHGVRL DPNGDQPPL |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | JEOL 2200FS |
---|---|
Specialist optics | Energy filter - Name: omega / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.2 mm |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |