[English] 日本語
Yorodumi
- EMDB-1120: Conservation of the capsid structure in tailed dsDNA bacteriophag... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1120
TitleConservation of the capsid structure in tailed dsDNA bacteriophages: the pseudoatomic structure of phi29.
Map dataThis map is a 3D cryo-EM reconstruction of a fiberless, isometric variant of bacteriophage phi29.
Sample
  • Sample: phi29 fiberless isometric particle
  • Virus: Bacillus phage phi29 (virus)
Biological speciesBacillus phage phi29 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsMorais MC / Choi KH / Koti JS / Chipman PR / Anderson DL / Rossmann MG
CitationJournal: Mol Cell / Year: 2005
Title: Conservation of the capsid structure in tailed dsDNA bacteriophages: the pseudoatomic structure of phi29.
Authors: Marc C Morais / Kyung H Choi / Jaya S Koti / Paul R Chipman / Dwight L Anderson / Michael G Rossmann /
Abstract: Bacteriophage phi29 is one of the smallest and simplest known dsDNA phages, making it amenable to structural investigations. The three-dimensional structure of a fiberless, isometric variant has been ...Bacteriophage phi29 is one of the smallest and simplest known dsDNA phages, making it amenable to structural investigations. The three-dimensional structure of a fiberless, isometric variant has been determined to 7.9 A resolution by cryo-electron microscopy (cryo-EM), allowing the identification of alpha helices and beta sheets. Their arrangement indicates that the folds of the phi29 and bacteriophage HK97 capsid proteins are similar except for an additional immunoglobulin-like domain of the phi29 protein. An atomic model that incorporates these two domains fits well into the cryo-EM density of the T = 3, fiberless isometric phi29 particle, and cryo-EM structures of fibered isometric and fiberless prolate prohead phi29 particles at resolutions of 8.7 A and 12.7 A, respectively. Thus, phi29 joins the growing number of phages that utilize the HK97 capsid structure, suggesting that this protein fold may be as prevalent in capsids of dsDNA phages as the jelly roll fold is in eukaryotic viruses.
History
DepositionFeb 17, 2005-
Header (metadata) releaseApr 5, 2005-
Map releaseApr 26, 2005-
UpdateNov 7, 2012-
Current statusNov 7, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-1yxn
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1yxn
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1120.gif

Downloads & links

-
Map

FileDownload / File: emd_1120.map.gz / Format: CCP4 / Size: 82.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis map is a 3D cryo-EM reconstruction of a fiberless, isometric variant of bacteriophage phi29.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.84 Å/pix.
x 281 pix.
= 517.04 Å		1.84 Å/pix.
x 281 pix.
= 517.04 Å		1.84 Å/pix.
x 281 pix.
= 517.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.84 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 10.0 / Movie #1: 8
Minimum - Maximum-7.0043 - 18.995999999999999
Average (Standard dev.)0.558723 (±3.64087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-140-140-140
Dimensions281281281
Spacing281281281
CellA=B=C: 517.04 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.841.841.84
M x/y/z281281281
origin x/y/z0.0000.0000.000
length x/y/z517.040517.040517.040
α/β/γ90.00090.00090.000
start NX/NY/NZ-140-140-140
NX/NY/NZ281281281
MAP C/R/S213
start NC/NR/NS-140-140-140
NC/NR/NS281281281
D min/max/mean-7.00418.9960.559

-
Supplemental data

-
Sample components

-
Entire : phi29 fiberless isometric particle

EntireName: phi29 fiberless isometric particle
Components
  • Sample: phi29 fiberless isometric particle
  • Virus: Bacillus phage phi29 (virus)

-
Supramolecule #1000: phi29 fiberless isometric particle

SupramoleculeName: phi29 fiberless isometric particle / type: sample / ID: 1000 / Oligomeric state: particle forms an T3 icosahedron / Number unique components: 1
Molecular weightTheoretical: 8.97 MDa

-
Supramolecule #1: Bacillus phage phi29

SupramoleculeName: Bacillus phage phi29 / type: virus / ID: 1 / Name.synonym: phi29 / NCBI-ID: 10756 / Sci species name: Bacillus phage phi29 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes / Syn species name: phi29
Host (natural)Organism: Bacillus subtilis (bacteria) / synonym: BACTERIA(EUBACTERIA)
Molecular weightExperimental: 8.97 MDa
Virus shellShell ID: 1 / Diameter: 425 Å / T number (triangulation number): 3

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.8
Details: 25 mM Tris-HCl 5 mM MgCl2 50 mM NaCl 5 mM sodium azide
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureAverage: 90.0 K
Alignment procedureLegacy - Electron beam tilt params: 0
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 15 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle min: 0 / Tilt angle max: 0

-
Image processing

CTF correctionDetails: CTF correction included phase and amplitude correction for whole micrographs
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMPFT, POR, P3DR / Number images used: 5922

-
Atomic model buiding 1

SoftwareName: SITUS and EMFIT
DetailsProtocol: Rigid Body. The fitted molecule consists of two domains, an HK97-like domain and a bacterial immunoglobulin group 2-like domain (BIG2). The two domains were fitted separately.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Target criteria: correlation of laplacian filtered data for SITUS, and for EMFIT, target maximizes positive density around an atom, minimizes negative density, and minimizes clashes with neighboring olecules
Output model

PDB-1yxn:
Pseudo-atomic model of a fiberless isometric variant of bacteriophage phi29

+
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