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- EMDB-33372: Cryo-EM structure of the T=3 lake sinai virus 2 virus-like capsid... -

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Basic information

Entry
Database: EMDB / ID: EMD-33372
TitleCryo-EM structure of the T=3 lake sinai virus 2 virus-like capsid at pH 8.5
Map data
Sample
  • Virus: Lake Sinai virus 2
    • Protein or peptide: Capsid protein alpha
KeywordsVIRUS LIKE PARTICLE
Function / homologyViral coat protein subunit / Capsid protein alpha
Function and homology information
Biological speciesLake Sinai virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 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 8, 2023-
Map releaseFeb 8, 2023-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33372.png

Downloads & links

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Map

FileDownload / File: emd_33372.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-0.5936428 - 1.6592724
Average (Standard dev.)0.033203684 (±0.11077396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-255-255-255
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_33372_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_33372_half_map_2.map
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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: Capsid protein alpha

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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: Capsid protein alpha

MacromoleculeName: Capsid protein alpha / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lake Sinai virus 2
Molecular weightTheoretical: 57.344309 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

UniProtKB: Capsid protein alpha

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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: 19860
Startup modelType of model: INSILICO MODEL / In silico model: Ab initial in cisTEM
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19860
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC

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