[English] 日本語
Yorodumi
- EMDB-10568: Capsid-neck interface of native GTA particle, asymmetric reconstr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10568
TitleCapsid-neck interface of native GTA particle, asymmetric reconstruction
Map datacapsid-neck interface of native GTA particle, asymmetric reconstruction
Sample
  • Complex: Rhodobacter capsulatus DE442 gene transfer agent
    • Complex: Capsid
      • Complex: Head spike
        • Protein or peptide: Head spike base Rcc01079
        • Protein or peptide: Head spike fiber Rcc01080
      • Protein or peptide: Major capsid protein Rcc01687
    • Complex: Connector
      • Protein or peptide: Portal protein Rcc01684
      • Protein or peptide: Adaptor protein Rcc01688
    • Complex: Tail
      • Protein or peptide: Stopper protein Rcc01689
      • Protein or peptide: Tail terminator protein Rcc01690
Function / homology: / Phage capsid / Phage capsid family / : / : / Phage major capsid protein, HK97 family
Function and homology information
Biological speciesRhodobacter capsulatus DE442 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsBardy P / Fuzik T / Hrebik D / Pantucek R / Beatty JT / Plevka P
Funding support Czech Republic, 7 items
OrganizationGrant numberCountry
Ministry of Education (Czech Republic)LQ1601 Czech Republic
Ministry of Education (Czech Republic)LM2011033 Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0070 Czech Republic
Czech Science Foundation18-17810S Czech Republic
Czech Science Foundation15-21631Y Czech Republic
Grant Agency of the Czech Republic18-13064S Czech Republic
European Molecular Biology Organization3041 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-
UpdateJul 22, 2020-
Current statusJul 22, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0252
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0252
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10568.png

Downloads & links

-
Map

FileDownload / File: emd_10568.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcapsid-neck interface of native GTA particle, asymmetric reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 512 pix.
= 544.256 Å		1.06 Å/pix.
x 512 pix.
= 544.256 Å		1.06 Å/pix.
x 512 pix.
= 544.256 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: 0.0252 / Movie #1: 0.0252
Minimum - Maximum-0.02734459 - 0.068505734
Average (Standard dev.)0.0013006121 (±0.005556197)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 544.256 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z544.256544.256544.256
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0270.0690.001

-
Supplemental data

-
Sample components

+
Entire : Rhodobacter capsulatus DE442 gene transfer agent

EntireName: Rhodobacter capsulatus DE442 gene transfer agent
Components
  • Complex: Rhodobacter capsulatus DE442 gene transfer agent
    • Complex: Capsid
      • Complex: Head spike
        • Protein or peptide: Head spike base Rcc01079
        • Protein or peptide: Head spike fiber Rcc01080
      • Protein or peptide: Major capsid protein Rcc01687
    • Complex: Connector
      • Protein or peptide: Portal protein Rcc01684
      • Protein or peptide: Adaptor protein Rcc01688
    • Complex: Tail
      • Protein or peptide: Stopper protein Rcc01689
      • Protein or peptide: Tail terminator protein Rcc01690

+
Supramolecule #1: Rhodobacter capsulatus DE442 gene transfer agent

SupramoleculeName: Rhodobacter capsulatus DE442 gene transfer agent / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: capsid-neck interface of native GTA particle
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
Molecular weightTheoretical: 880 KDa

+
Supramolecule #2: Capsid

SupramoleculeName: Capsid / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 / Details: Oblate T=3 capsid
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)

+
Supramolecule #3: Head spike

SupramoleculeName: Head spike / type: complex / ID: 3 / Parent: 2 / Macromolecule list: #2-#3 / Details: penton protrusion of the capsid
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria) / Strain: Gene transfer agent

+
Supramolecule #4: Connector

SupramoleculeName: Connector / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5
Details: special 5-fold vertex of the capsid, interconnecting capsid to tail
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)

+
Supramolecule #5: Tail

SupramoleculeName: Tail / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #6-#7
Details: tubular structure interconnecting capsid to baseplate (host-recognition device), partial
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria) / Strain: Gene transfer agent

+
Macromolecule #1: Major capsid protein Rcc01687

MacromoleculeName: Major capsid protein Rcc01687 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
SequenceString: MKTETKARAG TGMPEGADPV AEVKTALAGF LKEVKGFQDD VKTRLQQQEE RVTMLQTKTY AGRHALAAAA TEEAPHQKAF AAYLRTGDDD GLRGLSLEGK ALNSAVAAEG GYLVDPQTSE TIRGVLRSTA SLRQIASVVN VEATSFDVLV DKTDMGSGWA SETAALSETA ...String:
MKTETKARAG TGMPEGADPV AEVKTALAGF LKEVKGFQDD VKTRLQQQEE RVTMLQTKTY AGRHALAAAA TEEAPHQKAF AAYLRTGDDD GLRGLSLEGK ALNSAVAAEG GYLVDPQTSE TIRGVLRSTA SLRQIASVVN VEATSFDVLV DKTDMGSGWA SETAALSETA TPQIDRITIP LHELAAMPKA SQRLLDDSAF DIETWLANRI ADKFARAEAA AFISGDGVDK PTGFLTKTKV ANGAWAWGSL GYVATGAAGD FAAVNASDAV VDLVYALGAE YRANASFVMN SKTAGAVRKM KDADGRFLWA DSLAAGEPAR LMGYPVLIAE DMPDIAANAY AIAFGDFGNG YTIAERPDLR VLRDPFSAKP HVLFYASKRV GGDVSDFAAI KLLKFAAS

+
Macromolecule #2: Head spike base Rcc01079

MacromoleculeName: Head spike base Rcc01079 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
SequenceString:
MDVFAKHAVS LESPAVRHYE ITPSDSTDLA RRPRALRVQT GGTLVLRDET GITVTYTVFA GEILPVRPVR VLATGTTATA VGWE

+
Macromolecule #3: Head spike fiber Rcc01080

MacromoleculeName: Head spike fiber Rcc01080 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
SequenceString: MIALGLGLGL AANGGPALRR YAVNGVAPVA VLDFERHFLS HPLALTRATS ATYADALRAV QTAPADTPRY DYSTGKRALL LEASATNLLP NSAQFEAASW GKTRASVLAN AALAPNGTMT ADKLVEDTSN NSHFVARTGT QIAAGTSVTA SIFVKAAERR WFALVTADSA ...String:
MIALGLGLGL AANGGPALRR YAVNGVAPVA VLDFERHFLS HPLALTRATS ATYADALRAV QTAPADTPRY DYSTGKRALL LEASATNLLP NSAQFEAASW GKTRASVLAN AALAPNGTMT ADKLVEDTSN NSHFVARTGT QIAAGTSVTA SIFVKAAERR WFALVTADSA NAFRTTYFDL QTGTLGVVSQ GAAGHVAQIV AAGNGWYRCS VTQTQAASGN FNFYPSVASA NGATSYPGDG ASGLYLWGAQ LEAGAAVSSV IPTEAAAVTR AADLASVAVA AGSYDLRRVD AAGTAVTKGV AHPGGALTIG AGSLYLLSLF PAGAL

+
Macromolecule #4: Portal protein Rcc01684

MacromoleculeName: Portal protein Rcc01684 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
SequenceString: MGLNFFRKAA PEVRTEPVAE RKASVTGRIV AMASGAGRPV WGPRDTVSLM RTGFAGNPVG FRSVKLIAEA TAAVPLICQD AERRYEIHP VLDLLRRPNA GQGRAELFEA LIGQILLSGN GYLEAVCPEP GVPRELHVLR SDRMAVVPGA DGWPVGYDYT V GGRKHRFD ...String:
MGLNFFRKAA PEVRTEPVAE RKASVTGRIV AMASGAGRPV WGPRDTVSLM RTGFAGNPVG FRSVKLIAEA TAAVPLICQD AERRYEIHP VLDLLRRPNA GQGRAELFEA LIGQILLSGN GYLEAVCPEP GVPRELHVLR SDRMAVVPGA DGWPVGYDYT V GGRKHRFD MTGHPDPICH IKSFHPTDDH YGLSPMQAAA VALDVHNAAS AWSKALLDNA ARPSGAIIYK GADGQGVLAP EQ YERLIFE METHHQGARN AGRPMLLEGG LDWKPMGFSP SDMEFHETKA AAAREIALAF GVPPMLIGIP GDATYANYAE ANR AFYRLT VLPLLTRVSA ALAWWLSGYL GAQIELKPDL DQVPALAVER DQLWARIGAA GFLSNSEKRV LLGLPPTAEG

+
Macromolecule #5: Adaptor protein Rcc01688

MacromoleculeName: Adaptor protein Rcc01688 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
SequenceString: MMLNEVTAVP GTALPVAEFR DHLRLGTGFA DLGAEDAALL SYLRAAIAAI EGRTAKALIS RGFRLALTAW RWGDMQTLPI APVATVTAL RLVDAAGVET PVAAGWRLVP DMARPRIEAL GAMLPMIPTG GRVEIDFTAG FGASWSALPV DLAQAVFLLA A QYYELRHD ...String:
MMLNEVTAVP GTALPVAEFR DHLRLGTGFA DLGAEDAALL SYLRAAIAAI EGRTAKALIS RGFRLALTAW RWGDMQTLPI APVATVTAL RLVDAAGVET PVAAGWRLVP DMARPRIEAL GAMLPMIPTG GRVEIDFTAG FGASWSALPV DLAQAVFLLA A QYYELRHD GAAEGGAMPF GVMALIERWR TVRVLGGRP

+
Macromolecule #6: Stopper protein Rcc01689

MacromoleculeName: Stopper protein Rcc01689 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
SequenceString:
MSRPRLNRLL VLEEAVRVAD GAGGHRLDWQ AKGEVWAEVT AGSGSERAGE FVTLASVPFT IVVRAAPVGA ARRPRPEQRF REGARIFRI LAVAERDREG HYLSCFAREE VVA

+
Macromolecule #7: Tail terminator protein Rcc01690

MacromoleculeName: Tail terminator protein Rcc01690 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
SequenceString:
MSYAVAGALQ AAVYQQLRAD AVLAALVGTA VYDAVPPGPL AGTYVSLGPE DVADASDKTG AGAVHDFVIS VITDAAGFAT AKAAAAAVS DALVGADLVL SRGRLVGLWF LRAKARRVEK ADMRRIDLVF RARVEG

-
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
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: 39403
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0)
Details: relion_align_symmetry was used to shift map mass roughly into rotation center
Number images used: 35966
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 2.1) / Details: best class was selected for skip_align refinement
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