[English] 日本語
Yorodumi
- EMDB-34252: Cryo-EM model of the marine siphophage vB_DshS-R4C stopper-termin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34252
TitleCryo-EM model of the marine siphophage vB_DshS-R4C stopper-terminator complex
Map data
Sample
  • Virus: Dinoroseobacter phage vB_DshS-R4C (virus)
    • Protein or peptide: Head-to-tail joining protein
    • Protein or peptide: Major tail protein
    • Protein or peptide: Terminator protein
KeywordsMarine bacteriophage / Cryo-EM / Siphophage / Stopper protein / Terminator protein / Head-to-tail interface / VIRUS
Function / homology: / Head-to-tail joining protein / Minor tail protein / Major tail protein
Function and homology information
Biological speciesDinoroseobacter phage vB_DshS-R4C (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsHuang Y / Sun H / Wei S / Zheng Q / Li S / Zhang R / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Structure and proposed DNA delivery mechanism of a marine roseophage.
Authors: Yang Huang / Hui Sun / Shuzhen Wei / Lanlan Cai / Liqin Liu / Yanan Jiang / Jiabao Xin / Zhenqin Chen / Yuqiong Que / Zhibo Kong / Tingting Li / Hai Yu / Jun Zhang / Ying Gu / Qingbing Zheng ...Authors: Yang Huang / Hui Sun / Shuzhen Wei / Lanlan Cai / Liqin Liu / Yanan Jiang / Jiabao Xin / Zhenqin Chen / Yuqiong Que / Zhibo Kong / Tingting Li / Hai Yu / Jun Zhang / Ying Gu / Qingbing Zheng / Shaowei Li / Rui Zhang / Ningshao Xia /
Abstract: Tailed bacteriophages (order, Caudovirales) account for the majority of all phages. However, the long flexible tail of siphophages hinders comprehensive investigation of the mechanism of viral gene ...Tailed bacteriophages (order, Caudovirales) account for the majority of all phages. However, the long flexible tail of siphophages hinders comprehensive investigation of the mechanism of viral gene delivery. Here, we report the atomic capsid and in-situ structures of the tail machine of the marine siphophage, vB_DshS-R4C (R4C), which infects Roseobacter. The R4C virion, comprising 12 distinct structural protein components, has a unique five-fold vertex of the icosahedral capsid that allows genome delivery. The specific position and interaction pattern of the tail tube proteins determine the atypical long rigid tail of R4C, and further provide negative charge distribution within the tail tube. A ratchet mechanism assists in DNA transmission, which is initiated by an absorption device that structurally resembles the phage-like particle, RcGTA. Overall, these results provide in-depth knowledge into the intact structure and underlining DNA delivery mechanism for the ecologically important siphophages.
History
DepositionSep 8, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_34252.png

Downloads & links

-
Map

FileDownload / File: emd_34252.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 240 pix.
= 270.72 Å		1.13 Å/pix.
x 240 pix.
= 270.72 Å		1.13 Å/pix.
x 240 pix.
= 270.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.128 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0192
Minimum - Maximum-0.046572454 - 0.07828137
Average (Standard dev.)-0.00043931926 (±0.0078806495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 270.72 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_34252_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_34252_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Dinoroseobacter phage vB_DshS-R4C

EntireName: Dinoroseobacter phage vB_DshS-R4C (virus)
Components
  • Virus: Dinoroseobacter phage vB_DshS-R4C (virus)
    • Protein or peptide: Head-to-tail joining protein
    • Protein or peptide: Major tail protein
    • Protein or peptide: Terminator protein

-
Supramolecule #1: Dinoroseobacter phage vB_DshS-R4C

SupramoleculeName: Dinoroseobacter phage vB_DshS-R4C / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2590919 / Sci species name: Dinoroseobacter phage vB_DshS-R4C / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)

-
Macromolecule #1: Head-to-tail joining protein

MacromoleculeName: Head-to-tail joining protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter phage vB_DshS-R4C (virus)
Molecular weightTheoretical: 10.946397 KDa
SequenceString:
MIESLADWSI FTDPDVFGEP VTWTTPPLPD PVPAIFTDAS EDRPATLGPG VLTIAPTLTL GAAQLPFSPA RNHRCTVRGI TYRVAEVQP DGSGGLRLLL ERV

UniProtKB: Head-to-tail joining protein

-
Macromolecule #2: Major tail protein

MacromoleculeName: Major tail protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter phage vB_DshS-R4C (virus)
Molecular weightTheoretical: 13.574816 KDa
SequenceString:
MLKGKDGVVK NASTGDSIGH LQSWALDTQR DEVSGWGMGD DAERAFTTVG RASGNFEVYL DPADPSDDLE PGDLVDLELY PGGESTGSG YRSVAGALIL STAESASKDG IPMLTVNWRT SGALPQKATV S

UniProtKB: Major tail protein

-
Macromolecule #3: Terminator protein

MacromoleculeName: Terminator protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter phage vB_DshS-R4C (virus)
Molecular weightTheoretical: 14.866825 KDa
SequenceString:
MSEAIIAAAR GRLISPPFSD ATGDVYRTPE AALPAIIVEL DYTDAERISM GGGFIASAEL RVEILAKRDD WSLLTPTPAN TAEGMARLA ALVRTAILAP PSDLSGLAWS IAPAGYEFET ERGETPLARA TQSFALQILQ P

UniProtKB: Minor tail protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON III (4k 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: 1.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER / Details: trRosetta server
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5844
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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