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- EMDB-33380: Focused refinement cryo-EM map of the A/B/C subunits of the T=4 l... -

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Basic information

Entry
Database: EMDB / ID: EMD-33380
TitleFocused refinement cryo-EM map of the A/B/C subunits of the T=4 lake sinai virus 2 virus-like particle at pH 8.5
Map data
Sample
  • Virus: Lake Sinai virus 2
    • Protein or peptide: Lake sinai virus 2 capsid protein
KeywordsVIRUS LIKE PARTICLE
Biological speciesLake Sinai virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.44 Å
AuthorsChen NC / Wang CH / Chen CJ / Yoshimura M / Guan HH / Chuankhayan P / Lin CC
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: 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
DepositionMay 4, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33380.png

Downloads & links

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Map

FileDownload / File: emd_33380.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 512 pix.
= 539.494 Å		1.05 Å/pix.
x 512 pix.
= 539.494 Å		1.05 Å/pix.
x 512 pix.
= 539.494 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0537 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.33290672 - 1.713941
Average (Standard dev.)0.045675054 (±0.07769233)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 539.4944 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33380_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_33380_half_map_2.map
Projections & Slices
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Sample components

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Entire : Lake Sinai virus 2

EntireName: Lake Sinai virus 2
Components
  • Virus: Lake Sinai virus 2
    • Protein or peptide: Lake sinai virus 2 capsid protein

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Supramolecule #1: Lake Sinai virus 2

SupramoleculeName: 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

MacromoleculeName: Lake sinai virus 2 capsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Lake Sinai virus 2
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Particle selectionNumber selected: 17436
Startup modelType of model: INSILICO MODEL / In silico model: Ab initial in cisTEM
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17436
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC

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