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Yorodumi- EMDB-33370: Cryo-EM structure of the T=3 lake sinai virus 2 virus-like capsid... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33370 | |||||||||
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Title | Cryo-EM structure of the T=3 lake sinai virus 2 virus-like capsid at pH 6.5 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Viral coat protein subunit / Capsid protein alpha Function and homology information | |||||||||
Biological species | Lake Sinai virus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.74 Å | |||||||||
Authors | Chen NC / Wang CH / Chen CJ / Yoshimura M / Guan HH / Chuankhayan P / Lin CC | |||||||||
Funding support | Taiwan, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structures of honeybee-infecting Lake Sinai virus reveal domain functions and capsid assembly with dynamic motions Authors: Chen NC / Wang CH / Yoshimura M / Yeh YQ / Guan HH / Chuankhayan P / Lin CC / Lin PJ / Huang YC / Wakatsuki S / Ho MC / Chen CJ | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33370.map.gz | 482.9 MB | EMDB map data format | |
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Header (meta data) | emd-33370-v30.xml emd-33370.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_33370.png | 98.9 KB | ||
Others | emd_33370_half_map_1.map.gz emd_33370_half_map_2.map.gz | 473.6 MB 482.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33370 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33370 | HTTPS FTP |
-Related structure data
Related structure data | 7xpdMC 7xgzC 7xpaC 7xpbC 7xpeC 7xpfC 7xpgC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33370.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.0537 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33370_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33370_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Lake Sinai virus 2
Entire | Name: Lake Sinai virus 2 |
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Components |
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-Supramolecule #1: Lake Sinai virus 2
Supramolecule | Name: Lake Sinai virus 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1041831 / Sci species name: Lake Sinai virus 2 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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-Macromolecule #1: Capsid protein alpha
Macromolecule | Name: Capsid protein alpha / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Lake Sinai virus 2 |
Molecular weight | Theoretical: 57.344309 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MNPPTTTTTT TRTIRAPKVQ LTPNSATRRR RNRRRRRPAA AIAGPLSIQP SSINRRMVSR VTRRSAVVTA AGLAWLRQYL NPMGPDTTS VTGYPDGSAV TTCIADYSNT FNVSFPPREA LYCTGSSSSE KPTLVDADNY AKIDKWSNYD ITLCVLALPM L RNVVMLRL ...String: MNPPTTTTTT TRTIRAPKVQ LTPNSATRRR RNRRRRRPAA AIAGPLSIQP SSINRRMVSR VTRRSAVVTA AGLAWLRQYL NPMGPDTTS VTGYPDGSAV TTCIADYSNT FNVSFPPREA LYCTGSSSSE KPTLVDADNY AKIDKWSNYD ITLCVLALPM L RNVVMLRL YPHTPTAFAL TEQTPNFPQR FPNWSVYSAD GTRFNNGDEP GYLQSYVYLP NVDKHLSAAR GYRLLSRGIT GI FSAPALE TQGFVTACQY LAEGSIQSQS IKSDAVRSVT VNSDGTVKNV ESSSQTVSSM PRYVFPLDGD NCAPSSLTET YHQ AYQSKA TDGFYMPVLS SSRDNPFHPP QPRAIAVYGS FLARGCLDPV SEAHEADGPT HDIYRLNVAD DVAPLFNTGV VWFE GISPK FSLKLKTRTV LQYIPTSGSV LANFTRHEPT YDQIALDAAD RLRNLMPHAY PAAYNDWGWL GDLLDSAISM LPGVG TVYN IAKPLIKPAW NWLGNKVSDF FGNPVARDGD IFFDAK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.72 µm / Nominal defocus min: 0.25 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 46.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 41540 |
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Startup model | Type of model: INSILICO MODEL / In silico model: Ab initial in cisTEM |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cisTEM |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: cryoSPARC |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41540 |