[English] 日本語
Yorodumi
- PDB-6tsv: Tail of empty GTA particle computed with helical refinement, C6 s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tsv
TitleTail of empty GTA particle computed with helical refinement, C6 symmetry
ComponentsTail tube protein Rcc01691
KeywordsVIRUS / "helical refinement" / "gene transfer agent" / "bacteriophage" / "tail"
Function / homologyGene transfer agent, major tail protein / Phage major tail protein TP901-1 / Phage tail tube protein / Phage major tail protein, TP901-1 family
Function and homology information
Biological speciesRhodobacter capsulatus DE442 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsBardy, P. / Fuzik, T. / Hrebik, D. / Pantucek, R. / Beatty, J.T. / Plevka, P.
Funding support Czech Republic, 7items
OrganizationGrant numberCountry
Ministry of Education (Czech Republic)LQ1601 Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0070 Czech Republic
Ministry of Education (Czech Republic)LM2011033 Czech Republic
Czech Science Foundation15-21631Y Czech Republic
Czech Science Foundation18-17810S Czech Republic
European Molecular Biology Organization3041 Czech Republic
Grant Agency of the Czech Republic18-13064S Czech Republic
CitationJournal: Nat Commun / Year: 2020
Title: Structure and mechanism of DNA delivery of a gene transfer agent.
Authors: Pavol Bárdy / Tibor Füzik / Dominik Hrebík / Roman Pantůček / J Thomas Beatty / Pavel Plevka /
Abstract: Alphaproteobacteria, which are the most abundant microorganisms of temperate oceans, produce phage-like particles called gene transfer agents (GTAs) that mediate lateral gene exchange. However, the ...Alphaproteobacteria, which are the most abundant microorganisms of temperate oceans, produce phage-like particles called gene transfer agents (GTAs) that mediate lateral gene exchange. However, the mechanism by which GTAs deliver DNA into cells is unknown. Here we present the structure of the GTA of Rhodobacter capsulatus (RcGTA) and describe the conformational changes required for its DNA ejection. The structure of RcGTA resembles that of a tailed phage, but it has an oblate head shortened in the direction of the tail axis, which limits its packaging capacity to less than 4,500 base pairs of linear double-stranded DNA. The tail channel of RcGTA contains a trimer of proteins that possess features of both tape measure proteins of long-tailed phages from the family Siphoviridae and tail needle proteins of short-tailed phages from the family Podoviridae. The opening of a constriction within the RcGTA baseplate enables the ejection of DNA into bacterial periplasm.
History
DepositionDec 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Biological unit as author_defined_assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-10566
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10566
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Tail tube protein Rcc01691
A: Tail tube protein Rcc01691
C: Tail tube protein Rcc01691
D: Tail tube protein Rcc01691


Theoretical massNumber of molelcules
Total (without water)57,6804
Polymers57,6804
Non-polymers00
Water0
1
B: Tail tube protein Rcc01691
A: Tail tube protein Rcc01691
C: Tail tube protein Rcc01691
D: Tail tube protein Rcc01691
x 6


Theoretical massNumber of molelcules
Total (without water)346,08024
Polymers346,08024
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1
point symmetry operation5

-
Components

#1: Protein
Tail tube protein Rcc01691


Mass: 14420.007 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus DE442 (bacteria) / References: UniProt: D5ATZ7

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Rhodobacter capsulatus DE442 gene transfer agent tail tube
Type: COMPLEX
Details: tubular structure interconnecting head to baseplate (host recognition device), partial
Entity ID: all / Source: NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.35 MDaNO
210.35 MDaNO
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Rhodobacter capsulatus
Virus shellName: HK97-like oblate capsid / Diameter: 380 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.8 / Details: G-buffer, doi: 10.1016/0003-9861(77)90508-2
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTris1
21 mMNaClSodium chloride1
31 mMMgCl21
41 mMCaCl21
50.01 mg/mlBovine serum albumin1
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K

-
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 magnification: 75000 X / Nominal defocus max: -3000 nm / Nominal defocus min: -1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 42.75 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3114
Image scansWidth: 4096 / Height: 4096

-
Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
1RELION2.1particle selection
2EPU2.1image acquisition
4RELION2.1CTF correction
7Coot0.9model fitting
9RELION2.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 24.4 ° / Axial rise/subunit: 38.4 Å / Axial symmetry: C6
Particle selectionNum. of particles selected: 49821
3D reconstructionResolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49821 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d
ELECTRON MICROSCOPYf_angle_d1.17432712
ELECTRON MICROSCOPYf_dihedral_angle_d17.55614112
ELECTRON MICROSCOPYf_chiral_restr0.083648
ELECTRON MICROSCOPYf_plane_restr0.0064368

+
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