[English] 日本語
Yorodumi
- EMDB-10570: Tail tube of native GTA particle computed with C3 symmetry -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10570
TitleTail tube of native GTA particle computed with C3 symmetry
Map datatail tube with tape-measure protein of native GTA particle computed with C3 symmetry
Sample
  • Complex: Rhodobacter capsulatus DE442 gene transfer agent tail tube
    • Protein or peptide: Tail tube protein Rcc01691
    • Protein or peptide: Tape-measure protein Rcc01694
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 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.54 Å
AuthorsBardy P / Fuzik T / Hrebik D / Pantucek R / Beatty JT / Plevka P
Funding support Czech Republic, 7 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Czech Republic)LQ1601 Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0070 Czech Republic
Ministry of Education (MoE, Czech Republic)LM2011033 Czech Republic
Czech Science Foundation15-21631Y Czech Republic
Czech Science Foundation18-17810S Czech Republic
European Molecular Biology Organization (EMBO)3041 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, 2019-
Header (metadata) releaseJul 22, 2020-
Map releaseJul 22, 2020-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0288
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0288
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10570.png

Downloads & links

-
Map

FileDownload / File: emd_10570.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationtail tube with tape-measure protein of native GTA particle computed with C3 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 272.128 Å		1.06 Å/pix.
x 256 pix.
= 272.128 Å		1.06 Å/pix.
x 256 pix.
= 272.128 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0288 / Movie #1: 0.0288
Minimum - Maximum-0.023953356 - 0.063566454
Average (Standard dev.)0.0009116264 (±0.0046715625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 272.128 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z272.128272.128272.128
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0240.0640.001

-
Supplemental data

-
Sample components

-
Entire : Rhodobacter capsulatus DE442 gene transfer agent tail tube

EntireName: Rhodobacter capsulatus DE442 gene transfer agent tail tube
Components
  • Complex: Rhodobacter capsulatus DE442 gene transfer agent tail tube
    • Protein or peptide: Tail tube protein Rcc01691
    • Protein or peptide: Tape-measure protein Rcc01694

-
Supramolecule #1: Rhodobacter capsulatus DE442 gene transfer agent tail tube

SupramoleculeName: Rhodobacter capsulatus DE442 gene transfer agent tail tube
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: tubular structure interconnecting head to baseplate (host recognition device) composed out of 5 disks of tail tube hexamer. Inside tape-measure protein trimer is located.
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 500 KDa

-
Macromolecule #1: Tail tube protein Rcc01691

MacromoleculeName: Tail tube protein Rcc01691 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString:
MAAQNGKDLL IKLDLTGSGQ FETIAGLRAT RISFNAETVD VTSLESQGGW RELLGGAGVR SASISGAGVF KDADTDERAR QIFFDGEVPE FQVIIPDFGI VQGPFMITSI DYAGSHNGEA SYELAMASAG ALSFTAI

-
Macromolecule #2: Tape-measure protein Rcc01694

MacromoleculeName: Tape-measure protein Rcc01694 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString: MVEVDGLDGL GRQAAELERA LGGAEGVAAS FSDELGRMRE SLTYTGREVG TLSSSFGRSL RRAFDGVVFD GMKLSDALKT LAEGMSQAAY SVAMKPVQEA VGGALASTVN GLLGSVFGFA QGGAFSQGRV MPFAKGGVVS SPTSFPMRGA TGLMGEAGPE AILPLARAAD ...String:
MVEVDGLDGL GRQAAELERA LGGAEGVAAS FSDELGRMRE SLTYTGREVG TLSSSFGRSL RRAFDGVVFD GMKLSDALKT LAEGMSQAAY SVAMKPVQEA VGGALASTVN GLLGSVFGFA QGGAFSQGRV MPFAKGGVVS SPTSFPMRGA TGLMGEAGPE AILPLARAAD GRLGVQAGGG RVVNVVMNVT TPDAAGFARS QGQIAAQVNR RLARGSRNA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration20 mg/mL
BufferpH: 7.8
Component:
ConcentrationNameFormula
10.0 mMTris
1.0 mMNaCl
1.0 mMMgCl2
1.0 mMCaCl2
0.01 mg/mlBovine serum albumin

Details: G-buffer, doi: 10.1016/0003-9861(77)90508-2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 11.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3114 / Average exposure time: 1.0 sec. / Average electron dose: 42.75 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -3.0 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 41806
CTF correctionSoftware - Name: RELION (ver. 2.1)
Startup modelType of model: INSILICO MODEL
In silico model: stochastic gradient descent in RELION 2.1 de novo
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Details: skip align from C6 reconstruction / Number images used: 27724
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 2.1)
Details: 3D classification according to central density of tape-measure protein, using angles from C6 reconstruction. Best class was 3D classified according to C3 symmetry, one class was manually ...Details: 3D classification according to central density of tape-measure protein, using angles from C6 reconstruction. Best class was 3D classified according to C3 symmetry, one class was manually rotated and classes were merged.
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