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- EMDB-33373: Cryo-EM structure of the T=3 lake sinai virus 1 (delta-N48) virus... -
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Open data
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Basic information
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Title | Cryo-EM structure of the T=3 lake sinai virus 1 (delta-N48) virus-like capsid at pH 6.5 | |||||||||
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![]() | VIRUS LIKE PARTICLE | |||||||||
Function / homology | Viral coat protein subunit / Capsid protein alpha![]() | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.51 Å | |||||||||
![]() | Chen NC / Wang CH / Chen CJ / Yoshimura M / Guan HH / Chuankhayan P / Lin CC | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 473.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.2 KB 15.2 KB | Display Display | ![]() |
Images | ![]() | 138.5 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() ![]() | 370.7 MB 370.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xpgMC ![]() 7xpaC ![]() 7xpbC ![]() 7xpdC ![]() 7xpeC ![]() 7xpfC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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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_33373_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33373_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Lake Sinai virus 2
Entire | Name: ![]() |
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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: #1 / 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: ![]() |
Molecular weight | Theoretical: 62.979355 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MNSICSLYCL FRRVMPYSSE ILSSTVYRPP FLATSGLFFT RDHYKFIIMN QQQINPAQRS LRPRAQSAPS RSARRRRNRR RRNPSTPAG TVALQPSRIT RRVVSNLARR PLTITTAGLA WLRQYLNPMG PSTSSVSGFP DGSAVTTCIA DYTNTFNISF P PREAIYCT ...String: MNSICSLYCL FRRVMPYSSE ILSSTVYRPP FLATSGLFFT RDHYKFIIMN QQQINPAQRS LRPRAQSAPS RSARRRRNRR RRNPSTPAG TVALQPSRIT RRVVSNLARR PLTITTAGLA WLRQYLNPMG PSTSSVSGFP DGSAVTTCIA DYTNTFNISF P PREAIYCT GSNSDEKPVM LDAATYAKID AWTKSDITLC ILALPMLRNV VMIRLYASTP TAFTLSEGVP NFVQRFPNWS AF TTEGKVL NNGDSPGYIQ SFVYLPNVDK HLSAARGFRL LSRGLTGIYT APSLETQGFV TACQYLAEGA LQTQTVGNDF VQS VEVNAD KTVKNVNGKR LHYSGPPKFV FPLEGDNCAP SSLVETYHQA YQARAVDGFY MPILSSSRDN PFISPKPQPI AVFN RWYYR GCLDPVPASK VADGPSQYYY DLNVADDVAP LYNTGVVWME GISSKFSLKL KTRTVIQYIP TSGSVLANFT RHEPT YDQV ALDAADRIRN MMPHAYPAAY NDWGWLGDLL DSTLSMLPGI GTAYRFAKPL IKPAWNWLGG KVSDFFGNPV SRDGDI YFD AK UniProtKB: Capsid protein alpha |
-Macromolecule #2: RNA (5'-R(P*UP*G)-3')
Macromolecule | Name: RNA (5'-R(P*UP*G)-3') / type: rna / ID: 2 / Number of copies: 3 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 606.414 Da |
Sequence | String: UG |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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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: ![]() |
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 |