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- EMDB-10592: Virion of empty GTA particle -

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Basic information

Entry
Database: EMDB / ID: EMD-10592
TitleVirion of empty GTA particle
Map datavirion of empty gene transfer agent (GTA) particle, C5 symmetry, 4-times binned
Sample
  • Virus: Rhodobacter capsulatus DE442 (bacteria)
    • Complex: Capsid
      • Protein or peptide: Phage major capsid protein, HK97 family
      • Protein or peptide: Uncharacterized protein
      • Protein or peptide: Uncharacterized protein
    • Complex: Head spike
    • Complex: Connector
      • Protein or peptide: Adaptor protein Rcc01688
      • Protein or peptide: Portal protein Rcc01684
    • Complex: Tail
      • Protein or peptide: Tail tube protein Rcc01691
      • Protein or peptide: Tail terminator protein Rcc01690
      • Protein or peptide: Stopper protein Rcc01689
Keywords"gene transfer agent" / "virion" / "genome release" / "HK97" / VIRUS
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 / Phage major tail protein TP901-1 ...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 / Phage major tail protein TP901-1 / Phage tail tube protein / Bacteriophage/Gene transfer agent portal protein / Phage portal protein / Phage capsid / Phage capsid family
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein / Phage portal protein, HK97 family / Phage major capsid 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 SB 1003 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.47 Å
AuthorsBardy P / Fuzik T
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
DepositionJan 7, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 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: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tui
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6tui
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10592.png

Downloads & links

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Map

FileDownload / File: emd_10592.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationvirion of empty gene transfer agent (GTA) particle, C5 symmetry, 4-times binned
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.25 Å/pix.
x 360 pix.
= 1530.72 Å		4.25 Å/pix.
x 360 pix.
= 1530.72 Å		4.25 Å/pix.
x 360 pix.
= 1530.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.252 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.06793668 - 0.17580289
Average (Standard dev.)0.00013210182 (±0.0054646144)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 1530.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.2524.2524.252
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z1530.7201530.7201530.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0680.1760.000

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Supplemental data

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Additional map: virion of empty gene transfer agent (GTA) particle,...

Fileemd_10592_additional_1.map
Annotationvirion of empty gene transfer agent (GTA) particle, map assembled from symmetrized subparticles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rhodobacter capsulatus DE442

EntireName: Rhodobacter capsulatus DE442 (bacteria)
Components
  • Virus: Rhodobacter capsulatus DE442 (bacteria)
    • Complex: Capsid
      • Protein or peptide: Phage major capsid protein, HK97 family
      • Protein or peptide: Uncharacterized protein
      • Protein or peptide: Uncharacterized protein
    • Complex: Head spike
    • Complex: Connector
      • Protein or peptide: Adaptor protein Rcc01688
      • Protein or peptide: Portal protein Rcc01684
    • Complex: Tail
      • Protein or peptide: Tail tube protein Rcc01691
      • Protein or peptide: Tail terminator protein Rcc01690
      • Protein or peptide: Stopper protein Rcc01689

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Supramolecule #1: Rhodobacter capsulatus DE442

SupramoleculeName: Rhodobacter capsulatus DE442 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 8.03 MDa
Virus shellShell ID: 1 / Name: HK97-like oblate capsid / Diameter: 945.0 Å / T number (triangulation number): 3

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Supramolecule #2: Capsid

SupramoleculeName: Capsid / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 / Details: Oblate T=3 capsid, empty
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 5.42 MDa

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Supramolecule #3: Head spike

SupramoleculeName: Head spike / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 / Details: penton protrusion of the capsid
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 80 KDa

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Supramolecule #4: Connector

SupramoleculeName: Connector / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5-#6
Details: special 5-fold vertex of the capsid, interconnecting capsid to tail
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 760 KDa

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Supramolecule #5: Tail

SupramoleculeName: Tail / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4, #7-#8
Details: tubular structure interconnecting capsid to baseplate (host-recognition device)
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 730 KDa

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Macromolecule #1: Phage major capsid protein, HK97 family

MacromoleculeName: Phage major capsid protein, HK97 family / type: protein_or_peptide / ID: 1 / Number of copies: 29 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 40.894988 KDa
SequenceString: MPEGADPVAE VKTALAGFLK EVKGFQDDVK TRLQQQEERV TMLQTKTYAG RHALAAAATE EAPHQKAFAA YLRTGDDDGL RGLSLEGKA LNSAVAAEGG YLVDPQTSET IRGVLRSTAS LRQIASVVNV EATSFDVLVD KTDMGSGWAS ETAALSETAT P QIDRITIP ...String:
MPEGADPVAE VKTALAGFLK EVKGFQDDVK TRLQQQEERV TMLQTKTYAG RHALAAAATE EAPHQKAFAA YLRTGDDDGL RGLSLEGKA LNSAVAAEGG YLVDPQTSET IRGVLRSTAS LRQIASVVNV EATSFDVLVD KTDMGSGWAS ETAALSETAT P QIDRITIP LHELAAMPKA SQRLLDDSAF DIETWLANRI ADKFARAEAA AFISGDGVDK PTGFLTKTKV ANGAWAWGSL GY VATGAAG DFAAVNASDA VVDLVYALGA EYRANASFVM NSKTAGAVRK MKDADGRFLW ADSLAAGEPA RLMGYPVLIA EDM PDIAAN AYAIAFGDFG NGYTIAERPD LRVLRDPFSA KPHVLFYASK RVGGDVSDFA AIKLLKFAA

UniProtKB: Phage major capsid protein, HK97 family

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Macromolecule #2: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 9.104348 KDa
SequenceString:
MDVFAKHAVS LESPAVRHYE ITPSDSTDLA RRPRALRVQT GGTLVLRDET GITVTYTVFA GEILPVRPVR VLATGTTATA VGWE

UniProtKB: Uncharacterized protein

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Macromolecule #3: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 32.996828 KDa
SequenceString: MIALGLGLGL AANGGPALRR YAVNGVAPVA VLDFERHFLS HPLALTRATS ATYADALRAV QTAPADTPRY DYSTGKRALL LEASATNLL PNSAQFEAAS WGKTRASVLA NAALAPNGTM TADKLVEDTS NNSHFVARTG TQIAAGTSVT ASIFVKAAER R WFALVTAD ...String:
MIALGLGLGL AANGGPALRR YAVNGVAPVA VLDFERHFLS HPLALTRATS ATYADALRAV QTAPADTPRY DYSTGKRALL LEASATNLL PNSAQFEAAS WGKTRASVLA NAALAPNGTM TADKLVEDTS NNSHFVARTG TQIAAGTSVT ASIFVKAAER R WFALVTAD SANAFRTTYF DLQTGTLGVV SQGAAGHVAQ IVAAGNGWYR CSVTQTQAAS GNFNFYPSVA SANGATSYPG DG ASGLYLW GAQLEAGAAV SSVIPTEAAA VTRAADLASV AVAAGSYDLR RVDAAGTAVT KGVAHPGGAL TIGAGSLYLL SLF PAGAL

UniProtKB: Uncharacterized protein

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Macromolecule #4: Tail tube protein Rcc01691

MacromoleculeName: Tail tube protein Rcc01691 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (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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Macromolecule #5: Adaptor protein Rcc01688

MacromoleculeName: Adaptor protein Rcc01688 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (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 #6: Portal protein Rcc01684

MacromoleculeName: Portal protein Rcc01684 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (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 #7: Tail terminator protein Rcc01690

MacromoleculeName: Tail terminator protein Rcc01690 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (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 #8: Stopper protein Rcc01689

MacromoleculeName: Stopper protein Rcc01689 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (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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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 / 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

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Image processing

Particle selectionNumber selected: 6277
Startup modelType of model: INSILICO MODEL / Details: gradient descent method implemented in RELION
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 10.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 6277
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6tui:
Virion of empty GTA particle

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