[English] 日本語
Yorodumi
- PDB-8ucr: PhiCb5 maturation protein with Caulobacter crescentus bNY30a pili -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ucr
TitlePhiCb5 maturation protein with Caulobacter crescentus bNY30a pili
Components
  • Flp family type IVb pilin
  • Maturation protein
KeywordsRECOMBINATION / RNA phage / protein fibril
Function / homologyFlp/Fap pilin component / Flp/Fap pilin component / Assembly protein / Phage maturation protein / virion attachment to host cell pilus / virion component / membrane / Flp family type IVb pilin / Maturation protein
Function and homology information
Biological speciesCaulobacter phage phiCb5 (virus)
Caulobacter vibrioides (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.45 Å
AuthorsWang, Y. / Zhang, J.
Funding support United States, 1items
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
DepositionSep 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
MT: Maturation protein
A: Flp family type IVb pilin
X: Flp family type IVb pilin
Z: Flp family type IVb pilin
a: Flp family type IVb pilin
b: Flp family type IVb pilin
c: Flp family type IVb pilin
d: Flp family type IVb pilin
e: Flp family type IVb pilin
f: Flp family type IVb pilin
g: Flp family type IVb pilin
h: Flp family type IVb pilin
i: Flp family type IVb pilin
j: Flp family type IVb pilin
k: Flp family type IVb pilin
l: Flp family type IVb pilin
m: Flp family type IVb pilin


Theoretical massNumber of molelcules
Total (without water)110,79217
Polymers110,79217
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Maturation protein


Mass: 40725.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caulobacter phage phiCb5 (virus) / References: UniProt: D7RIC1
#2: Protein/peptide
Flp family type IVb pilin


Mass: 4379.140 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Caulobacter vibrioides (bacteria) / References: UniProt: A0A290MFS9

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: A complex of pilus and phiCb5 maturation protein / Type: COMPLEX
Details: A complex of Caulobacter crescentus pilus and ssRNA phage phiCb5 maturation protein in buffer
Entity ID: all / Source: NATURAL
Molecular weightValue: 0.21 MDa / Experimental value: NO
Source (natural)Organism: Caulobacter vibrioides (bacteria)
Buffer solutionpH: 7.5 / Details: 20mM tris, 2mM MgCl2
Buffer component
IDConc.NameFormulaBuffer-ID
12 mMMagnesium chlorideMgCl21
220 mMTrisC4H11NO31
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 25000 nm / Nominal defocus min: 5000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.17.1_3660: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56330 / Symmetry type: POINT

+
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