[English] 日本語
Yorodumi
- EMDB-36127: In situ structures of the ultra-long contracted tail of Myovirida... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36127
TitleIn situ structures of the ultra-long contracted tail of Myoviridae phage P1
Map data
Sample
  • Virus: Escherichia phage P1 (virus)
    • Protein or peptide: Gp22
KeywordsComplex / Virus / Phage / VIRAL PROTEIN
Function / homologyGp22
Function and homology information
Biological speciesEscherichia phage P1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsZhou JQ / Liu HR
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32071209 China
CitationJournal: Viruses / Year: 2023
Title: In Situ Structures of the Ultra-Long Extended and Contracted Tail of Myoviridae Phage P1.
Authors: Fan Yang / Liwen Wang / Junquan Zhou / Hao Xiao / Hongrong Liu /
Abstract: The phage tail is a common component of contractile injection systems (CISs), essential for exerting contractile function and facilitating membrane penetration of the inner tail tube. The near- ...The phage tail is a common component of contractile injection systems (CISs), essential for exerting contractile function and facilitating membrane penetration of the inner tail tube. The near-atomic resolution structures of the tail have been extensively studied, but the dynamic conformational changes before and after contraction and the associated molecular mechanism are still unclear. Here, we present the extended and contracted intact tail-structures of phage P1 by cryo-EM. The ultra-long tail of P1, 2450 Å in length, consists of a neck, a tail terminator, 53 repeated tail sheath rings, 53 repeated tube rings, and a baseplate. The sheath of the contracted tail shrinks by approximately 55%, resulting in the separation of the inner rigid tail tube from the sheath. The extended and contracted tails were further resolved by local reconstruction at 3.3 Å and 3.9 Å resolutions, respectively, allowing us to build the atomic models of the tail terminator protein gp24, the tube protein BplB, and the sheath protein gp22 for the extended tail, and of the sheath protein gp22 for the contracted tail. Our atomic models reveal the complex interaction network in the ultra-long tail and the novel conformational changes of the tail sheath between extended and contracted states. Our structures provide insights into the contraction and stabilization mechanisms of the tail.
History
DepositionMay 6, 2023-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_36127.png

Downloads & links

-
Map

FileDownload / File: emd_36127.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.018196661 - 0.056659944
Average (Standard dev.)0.0007058572 (±0.0050511383)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 489.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_36127_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_36127_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Escherichia phage P1

EntireName: Escherichia phage P1 (virus)
Components
  • Virus: Escherichia phage P1 (virus)
    • Protein or peptide: Gp22

-
Supramolecule #1: Escherichia phage P1

SupramoleculeName: Escherichia phage P1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2886926 / Sci species name: Escherichia phage P1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes

-
Macromolecule #1: Gp22

MacromoleculeName: Gp22 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage P1 (virus)
Molecular weightTheoretical: 56.989246 KDa
SequenceString: MSQYSIQQSL GNASGVAVSP INADATLSTG VALNSSLWAG IGVFARGKPF TVLAVTESNY EDVLGEPLKP SSGSQFEPIR HVYEAIQQT SGYVVRAVPD DAKFPIIMFD ESGEPAYSAL PYGSEIELDS GEAFAIYVDD GDPCISPTRE LTIETATADS A GNERFLLK ...String:
MSQYSIQQSL GNASGVAVSP INADATLSTG VALNSSLWAG IGVFARGKPF TVLAVTESNY EDVLGEPLKP SSGSQFEPIR HVYEAIQQT SGYVVRAVPD DAKFPIIMFD ESGEPAYSAL PYGSEIELDS GEAFAIYVDD GDPCISPTRE LTIETATADS A GNERFLLK LTQTTSLGVV TTLETHTVSL AEEAKDDMGR LCYLPTALEA RSKYLRAVVN EELISTAKVT NKKSLAFTGG TN GDQSKIS TAAYLRAVKV LNNAPYMYTA VLGLGCYDNA AITALGKICA DRLIDGFFDV KPTLTYAEAL PAVEDTGLLG TDY VSCSVY HYPFSCKDKW TQSRVVFGLS GVAYAAKARG VKKNSDVGGW HYSPAGEERA VIARASIQPL YPEDTPDEEA MVKG RLNKV SVGTSGQMII DDALTCCTQD NYLHFQHVPS LMNAISRFFV QLARQMKHSP DGITAAGLTK GMTKLLDRFV ASGAL VAPR DPDADGTEPY VLKVTQAEFD KWEVVWACCP TGVARRIQGV PLLIK

UniProtKB: Gp22

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8197
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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://pdbjlvh1.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