[English] 日本語
Yorodumi
- EMDB-42163: ssRNA phage PhiCb5 virion -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42163
TitlessRNA phage PhiCb5 virion
Map datamap
Sample
  • Complex: A complex of phiCb5 maturation protein and phiCb5 shell
    • Protein or peptide: Coat protein
    • Protein or peptide: Maturation protein
  • Ligand: CALCIUM IONCalcium
KeywordsssRNA phage / VIRUS
Function / homologyAssembly protein / Phage maturation protein / virion attachment to host cell pilus / virion component / viral capsid / Maturation protein / Coat protein
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria) / Caulobacter phage phiCb5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsWang Y / Zhang J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1R01GM141659 United States
CitationJournal: Sci Adv / Year: 2024
Title: Structural mechanisms of Tad pilus assembly and its interaction with an RNA virus.
Authors: Yuhang Wang / Matthew Theodore / Zhongliang Xing / Utkarsh Narsaria / Zihao Yu / Lanying Zeng / Junjie Zhang /
Abstract: Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV ... Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV pilins, Tad pilins lack the typical globular β sheet domain responsible for pilus assembly and phage binding. The mechanisms of Tad pilus assembly and its interaction with phage ΦCb5 have been elusive. Using cryo-electron microscopy, we unveiled the Tad pilus assembly mechanism, featuring a unique network of hydrogen bonds at its core. We then identified the Tad pilus binding to the ΦCb5 maturation protein (Mat) through its β region. Notably, the amino terminus of ΦCb5 Mat is exposed outside the capsid and phage/pilus interface, enabling the attachment of fluorescent and affinity tags. These engineered ΦCb5 virions can be efficiently assembled and purified in , maintaining infectivity against , which presents promising applications, including RNA delivery and phage display.
History
DepositionOct 1, 2023-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42163.png

Downloads & links

-
Map

FileDownload / File: emd_42163.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.0334
Minimum - Maximum-0.0049704043 - 1.7943912
Average (Standard dev.)0.006223467 (±0.056497477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 440.32 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half

Fileemd_42163_half_map_1.map
Annotationhalf
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half

Fileemd_42163_half_map_2.map
Annotationhalf
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : A complex of phiCb5 maturation protein and phiCb5 shell

EntireName: A complex of phiCb5 maturation protein and phiCb5 shell
Components
  • Complex: A complex of phiCb5 maturation protein and phiCb5 shell
    • Protein or peptide: Coat protein
    • Protein or peptide: Maturation protein
  • Ligand: CALCIUM IONCalcium

-
Supramolecule #1: A complex of phiCb5 maturation protein and phiCb5 shell

SupramoleculeName: A complex of phiCb5 maturation protein and phiCb5 shell
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: A complex of phiCb5 maturation protein and phiCb5 shell
Source (natural)Organism: Caulobacter vibrioides (bacteria)
Molecular weightTheoretical: 2.1 MDa

-
Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 178 / Enantiomer: LEVO
Source (natural)Organism: Caulobacter phage phiCb5 (virus)
Molecular weightTheoretical: 13.498981 KDa
SequenceString:
ALGDTLTITL GGSGGTAKVL RKINQDGYTS EYYLPETSSS FRAKVRHTKE SVKPNQVQYE RHNVEFTETV YASGSTPEFV RQAYVVIRH KVGDVSATVS DLGEALSFYL NEALYGKLIG WES

UniProtKB: Coat protein

-
Macromolecule #2: Maturation protein

MacromoleculeName: Maturation protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caulobacter phage phiCb5 (virus)
Molecular weightTheoretical: 40.725336 KDa
SequenceString: MARIRNRSSI ASSGMSTFYL FGTPIVNEEI IVRNTEWCSD VIGNPGDNPL DIHKQEWTIK PLSGQIIFGS GTYRSLQCPP EYCRGASLS HLSLPSQSGL GTTALARTNP SRPAFNLPAF IGELRDLPRM FKIAGDTMLR KGANAFLSYQ FGWKPLISDI S KALDFSAT ...String:
MARIRNRSSI ASSGMSTFYL FGTPIVNEEI IVRNTEWCSD VIGNPGDNPL DIHKQEWTIK PLSGQIIFGS GTYRSLQCPP EYCRGASLS HLSLPSQSGL GTTALARTNP SRPAFNLPAF IGELRDLPRM FKIAGDTMLR KGANAFLSYQ FGWKPLISDI S KALDFSAT VRTRSDEWHR LYSNGGLKRR INLGVDIEQK KENDVVLHSS NGFVVASHTV ITVRKTWATV RWRPDAGSLP PI TKSSSEK HARALLGLGV GGLIEGAWQL MPWSWMVDWF GNVGTFLQAS NNTIGASPGL VNIMTTTTTN HQFSVKRDLS DGW IKGGDC SATVTSKARS QSSGPTITAS IPNLSGRQLS ILGALGIQRV PRHLLR

UniProtKB: Maturation protein

-
Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 236 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
2.0 mMMgCl2Magnesium chloride
20.0 mMC4H11NO3Tris
3.0 mMCaCl2Calcium chloride

Details: 20mM tris, 2mM MgCl2, 3mM CaCl2
GridModel: C-flat-2/1
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 25.0 µm / Nominal defocus min: 5.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 272204
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://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