[English] 日本語
Yorodumi
- EMDB-5050: 11-fold assembly-naive P22 portal -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5050
Title11-fold assembly-naive P22 portal
Map data11 fold p22 portal
Sample
  • Sample: P22 gp1 subunit
  • Protein or peptide: gp1
Keywordsp22 bacteriophage phage portal virus connector
Methodsingle particle reconstruction / cryo EM / Resolution: 8.6 Å
AuthorsLander GC / Khayat R / Li R / Prevelige PE / Potter CS / Carragher B / Johnson JE
CitationJournal: Structure / Year: 2009
Title: The P22 tail machine at subnanometer resolution reveals the architecture of an infection conduit.
Authors: Gabriel C Lander / Reza Khayat / Rui Li / Peter E Prevelige / Clinton S Potter / Bridget Carragher / John E Johnson /
Abstract: The portal channel is a key component in the life cycle of bacteriophages and herpesviruses. The bacteriophage P22 portal is a 1 megadalton dodecameric oligomer of gp1 that plays key roles in capsid ...The portal channel is a key component in the life cycle of bacteriophages and herpesviruses. The bacteriophage P22 portal is a 1 megadalton dodecameric oligomer of gp1 that plays key roles in capsid assembly, DNA packaging, assembly of the infection machinery, and DNA ejection. The portal is the nucleation site for the assembly of 39 additional subunits generated from multiple copies of four gene products (gp4, gp10, gp9, and gp26), which together form the multifunctional tail machine. These components are organized with a combination of 12-fold (gp1, gp4), 6-fold (gp10, trimers of gp9), and 3-fold (gp26, gp9) symmetry. Here we present the 3-dimensional structures of the P22 assembly-naive portal formed from expressed subunits (gp1) and the intact tail machine purified from infectious virions. The assembly-naive portal structure exhibits a striking structural similarity to the structures of the portal proteins of SPP1 and phi29 derived from X-ray crystallography.
History
DepositionFeb 2, 2009-
Header (metadata) releaseFeb 4, 2009-
Map releaseJun 17, 2009-
UpdateJun 17, 2009-
Current statusJun 17, 2009Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5050_1.tif

Downloads & links

-
Map

FileDownload / File: emd_5050.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation11 fold p22 portal
Voxel sizeX=Y=Z: 1.95 Å
Density
Contour Level1: 1.2 / Movie #1: 1.1
Minimum - Maximum-3.12071 - 4.64816
Average (Standard dev.)0.000000000208784 (±0.352507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-72-72-72
Dimensions144144144
Spacing144144144
CellA=B=C: 280.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.951.951.95
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z280.800280.800280.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-20-28-19
NX/NY/NZ415638
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-3.1214.6480.000

-
Supplemental data

-
Sample components

-
Entire : P22 gp1 subunit

EntireName: P22 gp1 subunit
Components
  • Sample: P22 gp1 subunit
  • Protein or peptide: gp1

-
Supramolecule #1000: P22 gp1 subunit

SupramoleculeName: P22 gp1 subunit / type: sample / ID: 1000
Oligomeric state: heterogenous mixture of 11- and 12-fold rings
Number unique components: 1
Molecular weightExperimental: 910 KDa / Theoretical: 910 KDa

-
Macromolecule #1: gp1

MacromoleculeName: gp1 / type: protein_or_peptide / ID: 1 / Name.synonym: portal / Number of copies: 11 / Oligomeric state: 11-fold and 12-fold / Recombinant expression: Yes
Source (natural)Cell: e. coli strain bl21
Molecular weightExperimental: 82.7 KDa / Theoretical: 82.7 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.5
Details: 20mM Hepes, pH 7.5, 50 mM sodium chloride, 5mM beta-mercaptoethanol
GridDetails: C-flats from Protochips
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4.5 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: blot for 6 seconds, offset -2

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.4 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 80000
Sample stageSpecimen holder: gatan ct3500 / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 4.5 K
Alignment procedureLegacy - Astigmatism: corrected at 210,000 times mag
DateMay 13, 2008
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 20 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: each particle with EMAN
Final two d classificationNumber classes: 1000
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, SPIDER / Number images used: 22625
Detailsparticles selected using a difference of gaussians particle picker.

+
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