[English] 日本語
Yorodumi
- EMDB-33190: Cryo-EM structure of the T=4 lake sinai virus 2 virus-like capsid... -

+
Open data


ID or keywords:

Loading...

-
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 / homologyvirion component / Viral 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

-
Structure visualization

Supplemental images

emd_33190.png

Downloads & links

-
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 °

-
Supplemental data

-
Half map: #1

Fileemd_33190_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_33190_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Lake Sinai virus 2

EntireName: Lake Sinai virus 2
Components
  • Virus: Lake Sinai virus 2
    • Protein or peptide: Capsid protein alpha

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more