[English] 日本語
Yorodumi
- EMDB-3172: P22 bacteriophage GFP-loaded Procapsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3172
TitleP22 bacteriophage GFP-loaded Procapsid
Map dataReconstruction of bacteriophage P22 GFP-loaded Procapsid
Sample
  • Sample: Bacteriophage P22 GFP-loaded Procapsid
  • Virus: Enterobacteria phage P22 (virus)
  • Protein or peptide: Green Fluorescent protein
KeywordsP22 / bacteriophage / GFP / beta glucosidase / virus / AFM / cryoEM / cargo / nanocage
Biological speciesunidentified (others) / Enterobacteria phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 16.7 Å
AuthorsLlauro A / Luque D / Trus BL / Edwards E / Avera J / Reguera D / Douglas T / Pablo PJ / Caston JR
CitationJournal: Nanoscale / Year: 2016
Title: Cargo-shell and cargo-cargo couplings govern the mechanics of artificially loaded virus-derived cages.
Authors: Aida Llauró / Daniel Luque / Ethan Edwards / Benes L Trus / John Avera / David Reguera / Trevor Douglas / Pedro J de Pablo / José R Castón /
Abstract: Nucleic acids are the natural cargo of viruses and key determinants that affect viral shell stability. In some cases the genome structurally reinforces the shell, whereas in others genome packaging ...Nucleic acids are the natural cargo of viruses and key determinants that affect viral shell stability. In some cases the genome structurally reinforces the shell, whereas in others genome packaging causes internal pressure that can induce destabilization. Although it is possible to pack heterologous cargoes inside virus-derived shells, little is known about the physical determinants of these artificial nanocontainers' stability. Atomic force and three-dimensional cryo-electron microscopy provided mechanical and structural information about the physical mechanisms of viral cage stabilization beyond the mere presence/absence of cargos. We analyzed the effects of cargo-shell and cargo-cargo interactions on shell stability after encapsulating two types of proteinaceous payloads. While bound cargo to the inner capsid surface mechanically reinforced the capsid in a structural manner, unbound cargo diffusing freely within the shell cavity pressurized the cages up to ∼30 atm due to steric effects. Strong cargo-cargo coupling reduces the resilience of these nanocompartments in ∼20% when bound to the shell. Understanding the stability of artificially loaded nanocages will help to design more robust and durable molecular nanocontainers.
History
DepositionSep 29, 2015-
Header (metadata) releaseJan 20, 2016-
Map releaseFeb 1, 2017-
UpdateFeb 8, 2017-
Current statusFeb 8, 2017Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 12
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3172.png

Downloads & links

-
Map

FileDownload / File: emd_3172.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of bacteriophage P22 GFP-loaded 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: 12.0 / Movie #1: 12
Minimum - Maximum-60.505035399999997 - 85.849700929999997
Average (Standard dev.)1.58787704 (±11.842636110000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
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/NS000
NC/NR/NS180180180
D min/max/mean-60.50585.8501.588

-
Supplemental data

-
Sample components

-
Entire : Bacteriophage P22 GFP-loaded Procapsid

EntireName: Bacteriophage P22 GFP-loaded Procapsid
Components
  • Sample: Bacteriophage P22 GFP-loaded Procapsid
  • Virus: Enterobacteria phage P22 (virus)
  • Protein or peptide: Green Fluorescent protein

-
Supramolecule #1000: Bacteriophage P22 GFP-loaded Procapsid

SupramoleculeName: Bacteriophage P22 GFP-loaded Procapsid / type: sample / ID: 1000 / Oligomeric state: 60 / Number unique components: 2

-
Supramolecule #1: Enterobacteria phage P22

SupramoleculeName: Enterobacteria phage P22 / type: virus / ID: 1 / 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 subsp. enterica serovar Typhimurium (bacteria)
synonym: BACTERIA(EUBACTERIA)
Host systemOrganism: Escherichia coli (E. coli)
Virus shellShell ID: 1 / Diameter: 596 Å / T number (triangulation number): 7

-
Macromolecule #1: Green Fluorescent protein

MacromoleculeName: Green Fluorescent protein / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: unidentified (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

StainingType: NEGATIVE
Details: Samples were applied to grids, blotted and plunged into liquid ethane
GridDetails: R 2/2 Quantifoil grids
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC

-
Electron microscopy

MicroscopeFEI TECNAI F20
DateJan 15, 2015
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 346 / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 69444 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 69444
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Phase flipping & amplitude decay
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.7 Å / Resolution method: OTHER / Software - Name: Xmipp / Number images used: 7293

+
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