+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3693 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Arabis Mosaic Virus capsid protein | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Biological species | Arabis mosaic virus (isolate Syrah) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Lecorre F | |||||||||
Citation | Journal: To Be Published Title: Arabis Mosaic Virus capsid protein Authors: Lecorre F / Trapani S / Laikeehim J / Bron P | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3693.map.gz | 21 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3693-v30.xml emd-3693.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3693_fsc.xml | 17.9 KB | Display | FSC data file |
Images | emd_3693.png | 335.1 KB | ||
Others | emd_3693_half_map_1.map.gz emd_3693_half_map_2.map.gz | 283.2 MB 283.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3693 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3693 | HTTPS FTP |
-Validation report
Summary document | emd_3693_validation.pdf.gz | 441.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_3693_full_validation.pdf.gz | 440.5 KB | Display | |
Data in XML | emd_3693_validation.xml.gz | 20.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3693 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3693 | HTTPS FTP |
-Related structure data
Related structure data | 5nsi M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_3693.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Half map: #2
File | emd_3693_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_3693_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Arabis mosaic virus (isolate Syrah)
Entire | Name: Arabis mosaic virus (isolate Syrah) |
---|---|
Components |
|
-Supramolecule #1: Arabis mosaic virus (isolate Syrah)
Supramolecule | Name: Arabis mosaic virus (isolate Syrah) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 283676 / Sci species name: Arabis mosaic virus (isolate Syrah) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
---|---|
Host (natural) | Organism: Rubus odoratus (flowering raspberry) |
Host (natural) | Organism: Rheum rhabarbarum (garden rhubarb) |
Host system | Organism: Chenopodium quinoa (quinoa) |
-Macromolecule #1: RNA2 polyprotein
Macromolecule | Name: RNA2 polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Arabis mosaic virus (isolate Syrah) / Strain: isolate Syrah |
Molecular weight | Theoretical: 55.765406 KDa |
Recombinant expression | Organism: Chenopodium quinoa (quinoa) |
Sequence | String: GLAGRGTVPV PKDCQAGKYL KTLDLRDMVS GFSGIQYEKW ITAGLVMPDF KVVIRYPANA FTGITWVMSF DAYNRITSSI STTASPAYT LSVPHWLLHH KNGTTSCDID YGELCGHAMW FSATTFESPK LHFTCLTGNN KELAADWEFV VELYAEFEAA K SFLGKPNF ...String: GLAGRGTVPV PKDCQAGKYL KTLDLRDMVS GFSGIQYEKW ITAGLVMPDF KVVIRYPANA FTGITWVMSF DAYNRITSSI STTASPAYT LSVPHWLLHH KNGTTSCDID YGELCGHAMW FSATTFESPK LHFTCLTGNN KELAADWEFV VELYAEFEAA K SFLGKPNF IYSADAFNGS LKFLTIPPLE YDLSATSAYK SVSLLLGQTL VDGTHKVYNF NNTLLSYYLG IGGIVKGKVH VC SPCTYGI VLRVVSEWNG VTNNWNQLFK YPGCYIEEDG SFAIEIRSPY HRTPLRLIDA QSASSFTSTL NFYAISGPIA PSG ETAKMP VVVQIEEIAL PDLSVPSFPN DYFLWVDFSS FTVDVEEYVI GSRFFDISST TSTVALGDNP FSHMIACHGL HHGI LDLKL MWDLEGEFGK SSGGVTITKL CGDKATGMDG ASRVCALQNM GCETELYIGN YAGANPNTAL SLYSRWLAIK LDKAK SMKM LRILCKPRGN FEFYGRTCFK V |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 Component:
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 2.0 sec. / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient |
---|---|
Output model |
PDB-5nsi: |