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- EMDB-33190: Cryo-EM structure of the T=4 lake sinai virus 2 virus-like capsid... -

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Basic information

Entry
Database: EMDB / ID: EMD-33190
TitleCryo-EM structure of the T=4 lake sinai virus 2 virus-like capsid at pH 7.5
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: 3.24 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: 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
DepositionApr 7, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33190.png

Downloads & links

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Map

FileDownload / File: emd_33190.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0537 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.41222307 - 1.1936626
Average (Standard dev.)0.02750624 (±0.08699364)
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_33190_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33190_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: 4 / 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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
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: 30227
Startup modelType of model: INSILICO MODEL / In silico model: Ab initial in cisTEM
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30227
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC

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