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Yorodumi- EMDB-33375: Focus refinement cryo-EM map of the D/D/D subunits of the T=4 lak... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33375 | |||||||||
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Title | Focus refinement cryo-EM map of the D/D/D subunits of the T=4 lake sinai virus 2 virus-like particle | |||||||||
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Sample |
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Keywords | VIRUS LIKE PARTICLE | |||||||||
Biological species | Lake Sinai virus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.46 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: Nai-Chi Chen / Chun-Hsiung Wang / Masato Yoshimura / Yi-Qi Yeh / Hong-Hsiang Guan / Phimonphan Chuankhayan / Chien-Chih Lin / Pei-Ju Lin / Yen-Chieh Huang / Soichi Wakatsuki / Meng-Chiao Ho / Chun-Jung Chen / Abstract: Understanding the structural diversity of honeybee-infecting viruses is critical to maintain pollinator health and manage the spread of diseases in ecology and agriculture. We determine cryo-EM ...Understanding the structural diversity of honeybee-infecting viruses is critical to maintain pollinator health and manage the spread of diseases in ecology and agriculture. We determine cryo-EM structures of T = 4 and T = 3 capsids of virus-like particles (VLPs) of Lake Sinai virus (LSV) 2 and delta-N48 LSV1, belonging to tetraviruses, at resolutions of 2.3-2.6 Å in various pH environments. Structural analysis shows that the LSV2 capsid protein (CP) structural features, particularly the protruding domain and C-arm, differ from those of other tetraviruses. The anchor loop on the central β-barrel domain interacts with the neighboring subunit to stabilize homo-trimeric capsomeres during assembly. Delta-N48 LSV1 CP interacts with ssRNA via the rigid helix α1', α1'-α1 loop, β-barrel domain, and C-arm. Cryo-EM reconstructions, combined with X-ray crystallographic and small-angle scattering analyses, indicate that pH affects capsid conformations by regulating reversible dynamic particle motions and sizes of LSV2 VLPs. C-arms exist in all LSV2 and delta-N48 LSV1 VLPs across varied pH conditions, indicating that autoproteolysis cleavage is not required for LSV maturation. The observed linear domino-scaffold structures of various lengths, made up of trapezoid-shape capsomeres, provide a basis for icosahedral T = 4 and T = 3 architecture assemblies. These findings advance understanding of honeybee-infecting viruses that can cause Colony Collapse Disorder. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33375.map.gz | 254 MB | EMDB map data format | |
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Header (meta data) | emd-33375-v30.xml emd-33375.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_33375.png | 184.5 KB | ||
Filedesc metadata | emd-33375.cif.gz | 4.9 KB | ||
Others | emd_33375_half_map_1.map.gz emd_33375_half_map_2.map.gz | 473.7 MB 473.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33375 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33375 | HTTPS FTP |
-Validation report
Summary document | emd_33375_validation.pdf.gz | 974.7 KB | Display | EMDB validaton report |
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Full document | emd_33375_full_validation.pdf.gz | 974.3 KB | Display | |
Data in XML | emd_33375_validation.xml.gz | 19 KB | Display | |
Data in CIF | emd_33375_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33375 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33375 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33375.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_33375_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33375_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: Lake sinai virus 2 capsid protein
Macromolecule | Name: Lake sinai virus 2 capsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lake Sinai virus 2 |
Sequence | String: MNPPTTTTTT TRTIRAPKVQ LTPNSATRRR RNRRRRRPAA AIAGPLSIQP SSINRRMVSR VTRRSAVVTA AGLAWLRQYL NPMGPDTTSV TGYPDGSAVT TCIADYSNTF NVSFPPREAL YCTGSSSSEK PTLVDADNYA KIDKWSNYDI TLCVLALPML RNVVMLRLYP ...String: MNPPTTTTTT TRTIRAPKVQ LTPNSATRRR RNRRRRRPAA AIAGPLSIQP SSINRRMVSR VTRRSAVVTA AGLAWLRQYL NPMGPDTTSV TGYPDGSAVT TCIADYSNTF NVSFPPREAL YCTGSSSSEK PTLVDADNYA KIDKWSNYDI TLCVLALPML RNVVMLRLYP HTPTAFALTE QTPNFPQRFP NWSVYSADGT RFNNGDEPGY LQSYVYLPNV DKHLSAARGY RLLSRGITGI FSAPALETQG FVTACQYLAE GSIQSQSIKS DAVRSVTVNS DGTVKNVESS SQTVSSMPRY VFPLDGDNCA PSSLTETYHQ AYQSKATDGF YMPVLSSSRD NPFHPPQPRA IAVYGSFLAR GCLDPVSEAH EADGPTHDIY RLNVADDVAP LFNTGVVWFE GISPKFSLKL KTRTVLQYIP TSGSVLANFT RHEPTYDQIA LDAADRLRNL MPHAYPAAYN DWGWLGDLLD SAISMLPGVG TVYNIAKPLI KPAWNWLGNK VSDFFGNPVA RDGDIFFDAK |
-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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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 46.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.72 µm / Nominal defocus min: 0.25 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |