[English] 日本語
Yorodumi
- PDB-8ac6: Nudaurelia capensis omega virus maturation intermediate captured ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ac6
TitleNudaurelia capensis omega virus maturation intermediate captured at pH5.6 (insect cell expressed VLPs): medium class from symmetry expansion
Componentsp70
KeywordsVIRUS LIKE PARTICLE / ICOSAHEDRAL VIRUS / AUTO-CATALYTIC CLEAVAGE / VIRUS MATURATION / VIRUS-LIKE PARTICLE
Function / homologyPeptidase N2 / Peptidase family A21 / virion component / Viral coat protein subunit / p70
Function and homology information
Biological speciesNudaurelia capensis omega virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsCastells-Graells, R. / Hesketh, E.L. / Johnson, J.E. / Ranson, N.A. / Lawson, D.M. / Lomonossoff, G.P.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L014130/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9794 United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
CitationJournal: To be published
Title: Decoding virus maturation with cryo-EM structures of intermediates
Authors: Castells-Graells, R. / Hesketh, E.L. / Johnson, J.E. / Ranson, N.A. / Lawson, D.M. / Lomonossoff, G.P.
History
DepositionJul 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: p70
B: p70
C: p70
D: p70


Theoretical massNumber of molelcules
Total (without water)279,5684
Polymers279,5684
Non-polymers00
Water00
1
A: p70
B: p70
C: p70
D: p70
x 60


Theoretical massNumber of molelcules
Total (without water)16,774,069240
Polymers16,774,069240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

-
Components

#1: Protein
p70


Mass: 69891.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nudaurelia capensis omega virus / Cell (production host): Sf21 cell line / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4TVS9

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Nudaurelia capensis omega virus / Type: VIRUS / Details: expressed in Spodoptera frugiperda Sf21 cells / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 16.76 MDa / Experimental value: NO
Source (natural)Organism: Nudaurelia capensis omega virus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf21
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Gonimbrasia cytherea
Virus shellName: coat / Diameter: 425 nm / Triangulation number (T number): 4
Buffer solutionpH: 5.6 / Details: NULL
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: NULL
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 1 sec. / Electron dose: 49.1 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 16478
Details: Reconstructed from 2 datasets collected at doses of 48.7 and 50.4 electrons per Angstrom squared, respectively. The average of these two values is given.

-
Processing

EM software
IDNameVersionCategory
1RELION3.0.3particle selection
2EPUimage acquisition
4Gctf1.06CTF correction
7UCSF Chimera1.14model fitting
8Coot0.9model fitting
10RELION3.0.3initial Euler assignment
11RELION3.0.3final Euler assignment
12RELION3.0.3classification
13RELION3.0.33D reconstruction
14PHENIX1.20rc4model refinement
Image processingDetails: NULL
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 264917
Details: Particles from an I1 icosahedral consensus map (EMD-15266) were symmetry expanded to C1 and further 3D classified without alignment using a soft mask covering the icosahedral asymmetric unit. ...Details: Particles from an I1 icosahedral consensus map (EMD-15266) were symmetry expanded to C1 and further 3D classified without alignment using a soft mask covering the icosahedral asymmetric unit. The particles for this class were randomly split into half sets for the subsequent reconstruction and postprocessing steps. Note that the symmetry expansion step generates a 60-fold larger particle stack.
Symmetry type: POINT
Atomic model buildingB value: 126 / Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 8AAY

8aay


Accession code: 8AAY / Source name: PDB / Type: experimental model

+
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