[English] 日本語
Yorodumi
- EMDB-4387: Aged P22 Empty Procapsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4387
TitleAged P22 Empty Procapsid
Map dataAged P22 Empty Procapsid
Sample
  • Virus: Enterobacteria phage P22 (virus)
Biological speciesEnterobacteria phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 17.0 Å
AuthorsMcCoy K / Selivanovitch E / Luque D / Lee B / Edwards E / Caston JR / Douglas T
CitationJournal: Biomacromolecules / Year: 2018
Title: Cargo Retention inside P22 Virus-Like Particles.
Authors: Kimberly McCoy / Ekaterina Selivanovitch / Daniel Luque / Byeongdu Lee / Ethan Edwards / José R Castón / Trevor Douglas /
Abstract: Viral protein cages, with their regular and programmable architectures, are excellent platforms for the development of functional nanomaterials. The ability to transform a virus into a material with ...Viral protein cages, with their regular and programmable architectures, are excellent platforms for the development of functional nanomaterials. The ability to transform a virus into a material with intended structure and function relies on the existence of a well-understood model system, a noninfectious virus-like particle (VLP) counterpart. Here, we study the factors important to the ability of P22 VLP to retain or release various protein cargo molecules depending on the nature of the cargo, the capsid morphology, and the environmental conditions. Because the interaction between the internalized scaffold protein (SP) and the capsid coat protein (CP) is noncovalent, we have studied the efficiency with which a range of SP variants can dissociate from the interior of different P22 VLP morphologies and exit by traversing the porous capsid. Understanding the types of cargos that are either retained or released from the P22 VLP will aid in the rational design of functional nanomaterials.
History
DepositionApr 19, 2018-
Header (metadata) releaseMay 23, 2018-
Map releaseAug 22, 2018-
UpdateSep 19, 2018-
Current statusSep 19, 2018Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 24
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 24
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4387.png

Downloads & links

-
Map

FileDownload / File: emd_4387.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAged P22 Empty Procapsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.32 Å/pix.
x 180 pix.
= 777.6 Å		4.32 Å/pix.
x 180 pix.
= 777.6 Å		4.32 Å/pix.
x 180 pix.
= 777.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 24. / Movie #1: 24
Minimum - Maximum-55.790066000000003 - 83.083579999999998
Average (Standard dev.)1.181268 (±11.108878000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin909090
Dimensions180180180
Spacing180180180
CellA=B=C: 777.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.324.324.32
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z777.600777.600777.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS909090
NC/NR/NS180180180
D min/max/mean-55.79083.0841.181

-
Supplemental data

-
Sample components

-
Entire : Enterobacteria phage P22

EntireName: Enterobacteria phage P22 (virus)
Components
  • Virus: Enterobacteria phage P22 (virus)

-
Supramolecule #1: Enterobacteria phage P22

SupramoleculeName: Enterobacteria phage P22 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10754 / Sci species name: Enterobacteria phage P22 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Salmonella enterica (bacteria)
Host systemOrganism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2787
CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2xyy

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.33 CUT-OFF / Number images used: 2010
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: Xmipp
Final angle assignmentType: PROJECTION MATCHING / Software - Name: Xmipp

+
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