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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30793 | |||||||||
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Title | Capsid structure of human sapovirus | |||||||||
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Function / homology | ![]() RNA-protein covalent cross-linking / ribonucleoside triphosphate phosphatase activity / host cell cytoplasm / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Miyazaki N / Murakami K | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Atomic structure of human sapovirus capsid by single particle cryo-electron microscopy Authors: Miyazaki N / Murakami K / Oka T / Iwasaki K / Katayama K / Murata K | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 140.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.2 KB 10.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 19.8 KB | Display | ![]() |
Images | ![]() | 253.3 KB | ||
Filedesc metadata | ![]() | 5.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dodMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN
Supramolecule | Name: Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2169442 Sci species name: Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Calicivirin
Macromolecule | Name: Calicivirin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 60.753645 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MEGNGSQLGS RQHQESQAAV DPPGATGPTT SHVVVSNPEQ PNGPAQRLEM AVATGAIQSN VPEAIRNCFA VYRTFAWNDR MPAGTFLGS VSLHPNINPY TSHLSGMWAG WGGSFESRVS ISGSGVFAGR VVASVIPPGV DPSSIRDPGV LPHAFVDARI T EPVSFMIP ...String: MEGNGSQLGS RQHQESQAAV DPPGATGPTT SHVVVSNPEQ PNGPAQRLEM AVATGAIQSN VPEAIRNCFA VYRTFAWNDR MPAGTFLGS VSLHPNINPY TSHLSGMWAG WGGSFESRVS ISGSGVFAGR VVASVIPPGV DPSSIRDPGV LPHAFVDARI T EPVSFMIP DVRNTDYHRM DGNEPTCSLG LWVYQPLINP FSTSAVSTCW VSIETKPGGD FDFCLLKPPG QRMENGVSPE GL LPRRLGY ARGNRVGGLV VGLVLVADHH QVNRHFNANS ITYGWSTAPV NPMAAEIVVK HDYTNNRNAW LSIGAKNKGP LFP GLPNHF PDSCASTLVG AMDTGRHMPA TGVCGPAIGF QDNGDVFENE TPAVMFATFN PLTGGDNTNP IALYDSINPA SLAV MCTKS NSNFDSSGFA NDKNVVVQMS WEMYTNSQQI QGRVTPMQGT NFVFTSSGAN TLALWEERLL SYDGHQAILY SSQME RTSE YFQNDNVNIP PGSMAVFNVE TNSASFQIGI REDGYMVTGG TIGTHVVLDP ETRFQYVGLL PLTAALAGPN GNSGRA RRV FQ UniProtKB: ![]() |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average exposure time: 1.0 sec. / Average electron dose: 20.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |