[English] 日本語
Yorodumi
- EMDB-2375: Cryo-EM structure of T=1 SV40 VP1 VLP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2375
TitleCryo-EM structure of T=1 SV40 VP1 VLP
Map dataReconstruction of SV40 VP1 VLP
Sample
  • Sample: Reassembled SV40 VP1 VLP with 1.9 Knt RNA
  • Virus: Simian virus 40
  • RNA: Xenopus elongation factor RNA (1.9 Knt)
KeywordsSimian virus 40 / SV40 / VLP / T=1 icosahedral capsid / assembly mechanism / nucleic acid substrate
Biological speciesXenopus laevis (African clawed frog) / Simian virus 40
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsKler S / Wang JC-Y / Dhason RS / Zlotnick A / Oppenheim A
CitationJournal: ACS Chem Biol / Year: 2013
Title: Scaffold properties are a key determinant of the size and shape of self-assembled virus-derived particles.
Authors: Stanislav Kler / Joseph Che-Yen Wang / Mary Dhason / Ariella Oppenheim / Adam Zlotnick /
Abstract: Controlling the geometry of self-assembly will enable a greater diversity of nanoparticles than now available. Viral capsid proteins, one starting point for investigating self-assembly, have evolved ...Controlling the geometry of self-assembly will enable a greater diversity of nanoparticles than now available. Viral capsid proteins, one starting point for investigating self-assembly, have evolved to form regular particles. The polyomavirus SV40 assembles from pentameric subunits and can encapsidate anionic cargos. On short ssRNA (≤814 nt), SV40 pentamers form 22 nm diameter capsids. On RNA too long to fit a T = 1 particle, pentamers forms strings of 22 nm particles and heterogeneous particles of 29-40 nm diameter. However, on dsDNA SV40 forms 50 nm particles composed of 72 pentamers. A 7.2-Å resolution cryo-EM image reconstruction of 22 nm particles shows that they are built of 12 pentamers arranged with T = 1 icosahedral symmetry. At 3-fold vertices, pentamers each contribute to a three-helix triangle. This geometry of interaction is not seen in crystal structures of T = 7 viruses and provides a structural basis for the smaller capsids. We propose that the heterogeneous particles are actually mosaics formed by combining different geometries of interaction from T = 1 capsids and virions. Assembly can be trapped in novel conformations because SV40 interpentamer contacts are relatively strong. The implication is that by virtue of their large catalog of interactions, SV40 pentamers have the ability to self-assemble on and conform to a broad range of shapes.
History
DepositionMay 15, 2013-
Header (metadata) releaseMay 22, 2013-
Map releaseMar 26, 2014-
UpdateMar 26, 2014-
Current statusMar 26, 2014Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2375.jpg

Downloads & links

-
Map

FileDownload / File: emd_2375.map.gz / Format: CCP4 / Size: 30.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of SV40 VP1 VLP
Voxel sizeX=Y=Z: 1.8 Å
Density
Contour LevelBy AUTHOR: 2.7 / Movie #1: 2.7
Minimum - Maximum-16.75599098 - 11.54889202
Average (Standard dev.)0.22530594 (±1.46823072)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions201201201
Spacing201201201
CellA=B=C: 361.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.81.81.8
M x/y/z201201201
origin x/y/z0.0000.0000.000
length x/y/z361.800361.800361.800
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS201201201
D min/max/mean-16.75611.5490.225

-
Supplemental data

-
Sample components

-
Entire : Reassembled SV40 VP1 VLP with 1.9 Knt RNA

EntireName: Reassembled SV40 VP1 VLP with 1.9 Knt RNA
Components
  • Sample: Reassembled SV40 VP1 VLP with 1.9 Knt RNA
  • Virus: Simian virus 40
  • RNA: Xenopus elongation factor RNA (1.9 Knt)

-
Supramolecule #1000: Reassembled SV40 VP1 VLP with 1.9 Knt RNA

SupramoleculeName: Reassembled SV40 VP1 VLP with 1.9 Knt RNA / type: sample / ID: 1000 / Details: The sample was directly applied to the grid / Oligomeric state: 60 SV40 VP1 and one 1.9 Knt RNA / Number unique components: 2
Molecular weightTheoretical: 3.5 MDa

-
Supramolecule #1: Simian virus 40

SupramoleculeName: Simian virus 40 / type: virus / ID: 1 / Details: 1.9 Knt RNA was encapsidated inside the particle / NCBI-ID: 10633 / Sci species name: Simian virus 40 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Hominoidea (apes) / synonym: VERTEBRATES
Host systemOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: sf9 / Recombinant plasmid: pVL1393
Molecular weightTheoretical: 3 MDa
Virus shellShell ID: 1 / Name: VP1 / Diameter: 266 Å / T number (triangulation number): 60

-
Macromolecule #1: Xenopus elongation factor RNA (1.9 Knt)

MacromoleculeName: Xenopus elongation factor RNA (1.9 Knt) / type: rna / ID: 1 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Xenopus laevis (African clawed frog) / synonym: African clawed frog

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.2 / Details: 125 mM NaCl, 50 mM MOPS
GridDetails: Quantifoil R 2/2 holey carbon 200 mesh copper grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 4 seconds before plunging

-
Electron microscopy

MicroscopeOTHER
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.1 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 60000
Specialist opticsEnergy filter - Name: Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 97 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 60,000 times magnification
DetailsWeak beam illumination
DateJul 5, 2011
Image recordingNumber real images: 254 / Average electron dose: 14 e/Å2 / Details: Images were recorded on Gatan 4k x 4k CCD

-
Image processing

CTF correctionDetails: Each particle phase-flipping
Final angle assignmentDetails: PO2R refined angle 0.25 degree, center 0.1 degree
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 3511
DetailsThe particles were boxed with e2boxer.py and image processing was done by Auto3dem (v4.02)

-
Atomic model buiding 1

Initial modelPDB ID:

1sva

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
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