[English] 日本語
Yorodumi
- PDB-6toa: Neck of empty GTA particle computed with C6 symmetry -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6toa
TitleNeck of empty GTA particle computed with C6 symmetry
Components
  • Adaptor protein Rcc01688Adapter
  • Portal protein Rcc01684
  • Stopper protein Rcc01689
  • Tail terminator protein Rcc01690
  • Tail tube protein Rcc01691
KeywordsVIRUS / "neck" / "connector" / "portal" / "tail"
Function / homology
Function and homology information


Phage conserved hypothetical protein / Tail completion protein / Protein of unknown function (DUF3168) / Gene transfer agent, major tail protein / Phage portal protein, HK97 / Bacteriophage SPP1, head-tail adaptor / Phage head-tail joining protein / Bacteriophage SPP1, head-tail adaptor superfamily / Bacteriophage/Gene transfer agent portal protein / Phage portal protein ...Phage conserved hypothetical protein / Tail completion protein / Protein of unknown function (DUF3168) / Gene transfer agent, major tail protein / Phage portal protein, HK97 / Bacteriophage SPP1, head-tail adaptor / Phage head-tail joining protein / Bacteriophage SPP1, head-tail adaptor superfamily / Bacteriophage/Gene transfer agent portal protein / Phage portal protein / Phage major tail protein TP901-1 / Phage tail tube protein
Similarity search - Domain/homology
Phage portal protein, HK97 family / Gene transfer agent protein / Head-tail adaptor protein / DUF3168 domain-containing protein / Phage major tail protein, TP901-1 family
Similarity search - Component
Biological speciesRhodobacter capsulatus DE442 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 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 11, 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
  • Superimposition on EM map
  • EMDB-10542
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Adaptor protein Rcc01688
A: Portal protein Rcc01684
B: Portal protein Rcc01684
D: Adaptor protein Rcc01688
F: Tail terminator protein Rcc01690
E: Stopper protein Rcc01689
G: Tail tube protein Rcc01691


Theoretical massNumber of molelcules
Total (without water)168,3027
Polymers168,3027
Non-polymers00
Water0
1
C: Adaptor protein Rcc01688
A: Portal protein Rcc01684
B: Portal protein Rcc01684
D: Adaptor protein Rcc01688
F: Tail terminator protein Rcc01690
E: Stopper protein Rcc01689
G: Tail tube protein Rcc01691
x 6


Theoretical massNumber of molelcules
Total (without water)1,009,80942
Polymers1,009,80942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1
point symmetry operation5

-
Components

#1: Protein Adaptor protein Rcc01688 / Adapter


Mass: 20956.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus DE442 (bacteria) / References: UniProt: D5ATZ4
#2: Protein Portal protein Rcc01684


Mass: 42846.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus DE442 (bacteria) / References: UniProt: D5ATZ0
#3: Protein Tail terminator protein Rcc01690


Mass: 13871.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus DE442 (bacteria) / References: UniProt: D5ATZ6
#4: Protein Stopper protein Rcc01689


Mass: 12403.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus DE442 (bacteria) / References: UniProt: D5ATZ5
#5: Protein Tail tube protein Rcc01691


Mass: 14420.007 Da / Num. of mol.: 1 / 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: single particle reconstruction

-
Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Rhodobacter capsulatus DE442 gene transfer agent neckCOMPLEXneck region of empty particleall0NATURAL
2ConnectorCOMPLEXspecial 5-fold vertex of the capsid, interconnecting capsid to tail#1-#21NATURAL
3TailCOMPLEXtubular structure interconnecting capsid to baseplate (host-recognition device)#3-#51NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111.00 MDaNO
210.76 MDaNO
310.24 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Rhodobacter capsulatus DE442 (bacteria)1415160
32Rhodobacter capsulatus DE442 (bacteria)1415160
43Rhodobacter capsulatus DE442 (bacteria)1415160
Details of virus
IDEntity assembly-IDEmptyEnvelopedIsolateType
11YESNOSTRAINVIRUS-LIKE PARTICLE
22
33
Natural host
IDEntity assembly-IDOrganismNcbi tax-ID
11Rhodobacter capsulatus1061
12
13
Virus shell
IDEntity assembly-IDNameDiameter (nm)Triangulation number (T number)
11HK97-like oblate capsid3803
12
13
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
10RELION3final Euler assignment
11RELION2.1classification
12RELION33D reconstruction
19PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 49821
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49821 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d
ELECTRON MICROSCOPYf_angle_d1.12747325
ELECTRON MICROSCOPYf_dihedral_angle_d16.32220649
ELECTRON MICROSCOPYf_chiral_restr0.0655265
ELECTRON MICROSCOPYf_plane_restr0.0096222

+
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