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- EMDB-10542: Neck of empty GTA particle computed with C6 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-10542
TitleNeck of empty GTA particle computed with C6 symmetry
Map dataneck of empty GTA particle, C6 symmetrized
Sample
  • Complex: Rhodobacter capsulatus DE442 gene transfer agent neck
    • Complex: Connector
      • Protein or peptide: Adaptor protein Rcc01688
      • Protein or peptide: Portal protein Rcc01684
    • Complex: Tail
      • Protein or peptide: Tail terminator protein Rcc01690
      • Protein or peptide: Stopper protein Rcc01689
      • Protein or peptide: Tail tube protein Rcc01691
Keywords"neck" / "connector" / "portal" / "tail" / VIRUS
Function / homology
Function and homology information


Phage conserved hypothetical protein / Tail completion protein / Tail completion protein gp17 / 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 / Phage major tail protein TP901-1 ...Phage conserved hypothetical protein / Tail completion protein / Tail completion protein gp17 / 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 / Phage major tail protein TP901-1 / Phage tail tube protein / Bacteriophage/Gene transfer agent portal protein / Phage portal 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsBardy P / Fuzik T
Funding support Czech Republic, 7 items
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, 2019-
Header (metadata) releaseJul 22, 2020-
Map releaseJul 22, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.13
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.13
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6toa
  • Surface level: 0.13
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10542.png

Downloads & links

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Map

FileDownload / File: emd_10542.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationneck of empty GTA particle, C6 symmetrized
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 318.9 Å		1.06 Å/pix.
x 300 pix.
= 318.9 Å		1.06 Å/pix.
x 300 pix.
= 318.9 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: 0.13 / Movie #1: 0.13
Minimum - Maximum-0.34150982 - 0.62192845
Average (Standard dev.)0.0018720732 (±0.024020413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 318.9 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z318.900318.900318.900
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.3420.6220.002

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Supplemental data

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Sample components

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Entire : Rhodobacter capsulatus DE442 gene transfer agent neck

EntireName: Rhodobacter capsulatus DE442 gene transfer agent neck
Components
  • Complex: Rhodobacter capsulatus DE442 gene transfer agent neck
    • Complex: Connector
      • Protein or peptide: Adaptor protein Rcc01688
      • Protein or peptide: Portal protein Rcc01684
    • Complex: Tail
      • Protein or peptide: Tail terminator protein Rcc01690
      • Protein or peptide: Stopper protein Rcc01689
      • Protein or peptide: Tail tube protein Rcc01691

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Supramolecule #1: Rhodobacter capsulatus DE442 gene transfer agent neck

SupramoleculeName: Rhodobacter capsulatus DE442 gene transfer agent neck / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: neck region of empty particle
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
Molecular weightTheoretical: 240 KDa

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Supramolecule #2: Connector

SupramoleculeName: Connector / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Details: special 5-fold vertex of the capsid, interconnecting capsid to tail
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)

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Supramolecule #3: Tail

SupramoleculeName: Tail / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#5
Details: tubular structure interconnecting capsid to baseplate (host-recognition device)
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)

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Macromolecule #1: Adaptor protein Rcc01688

MacromoleculeName: Adaptor protein Rcc01688 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
Molecular weightTheoretical: 20.956354 KDa
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

UniProtKB: Gene transfer agent protein

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Macromolecule #2: Portal protein Rcc01684

MacromoleculeName: Portal protein Rcc01684 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
Molecular weightTheoretical: 42.84691 KDa
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

UniProtKB: Phage portal protein, HK97 family

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Macromolecule #3: Tail terminator protein Rcc01690

MacromoleculeName: Tail terminator protein Rcc01690 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
Molecular weightTheoretical: 13.871859 KDa
SequenceString:
MSYAVAGALQ AAVYQQLRAD AVLAALVGTA VYDAVPPGPL AGTYVSLGPE DVADASDKTG AGAVHDFVIS VITDAAGFAT AKAAAAAVS DALVGADLVL SRGRLVGLWF LRAKARRVEK ADMRRIDLVF RARVEG

UniProtKB: DUF3168 domain-containing protein

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Macromolecule #4: Stopper protein Rcc01689

MacromoleculeName: Stopper protein Rcc01689 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
Molecular weightTheoretical: 12.403123 KDa
SequenceString:
MSRPRLNRLL VLEEAVRVAD GAGGHRLDWQ AKGEVWAEVT AGSGSERAGE FVTLASVPFT IVVRAAPVGA ARRPRPEQRF REGARIFRI LAVAERDREG HYLSCFAREE VVA

UniProtKB: Head-tail adaptor protein

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Macromolecule #5: Tail tube protein Rcc01691

MacromoleculeName: Tail tube protein Rcc01691 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
Molecular weightTheoretical: 14.420007 KDa
SequenceString:
MAAQNGKDLL IKLDLTGSGQ FETIAGLRAT RISFNAETVD VTSLESQGGW RELLGGAGVR SASISGAGVF KDADTDERAR QIFFDGEVP EFQVIIPDFG IVQGPFMITS IDYAGSHNGE ASYELAMASA GALSFTAI

UniProtKB: Phage major tail protein, TP901-1 family

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV

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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

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Image processing

Particle selectionNumber selected: 49821
Startup modelType of model: INSILICO MODEL
In silico model: stochastic gradient descent in RELION 2.1 de novo
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 49821
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6toa:
Neck of empty GTA particle computed with C6 symmetry

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