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- EMDB-10571: Baseplate of empty GTA particle computed with C3 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-10571
TitleBaseplate of empty GTA particle computed with C3 symmetry
Map databaseplate of empty GTA particle computed with C3 symmetry
Sample
  • Complex: Rhodobacter capsulatus DE442 gene transfer agent baseplate
    • Protein or peptide: Putative gene transfer agent protein
    • Protein or peptide: Putative gene transfer agent protein
    • Protein or peptide: Putative gene transfer agent protein
    • Protein or peptide: Tail fiber protein Rcc00171
Function / homology
Function and homology information


Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Phage conserved hypothetical protein BR0599 / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Tip attachment protein J ...Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Phage conserved hypothetical protein BR0599 / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Tip attachment protein J / Putative phage tail protein / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Putative gene transfer agent protein / Putative gene transfer agent protein / Putative gene transfer agent protein
Similarity search - Component
Biological speciesRhodobacter capsulatus DE442 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.49 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

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0557
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0557
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10571.png

Downloads & links

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Map

FileDownload / File: emd_10571.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationbaseplate of empty GTA particle computed with C3 symmetry
Voxel sizeX=Y=Z: 1.063 Å
Density
Contour LevelBy AUTHOR: 0.0557 / Movie #1: 0.0557
Minimum - Maximum-0.11004337 - 0.39625853
Average (Standard dev.)0.0014252156 (±0.009959277)
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-0.1100.3960.001

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Supplemental data

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Sample components

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Entire : Rhodobacter capsulatus DE442 gene transfer agent baseplate

EntireName: Rhodobacter capsulatus DE442 gene transfer agent baseplate
Components
  • Complex: Rhodobacter capsulatus DE442 gene transfer agent baseplate
    • Protein or peptide: Putative gene transfer agent protein
    • Protein or peptide: Putative gene transfer agent protein
    • Protein or peptide: Putative gene transfer agent protein
    • Protein or peptide: Tail fiber protein Rcc00171

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Supramolecule #1: Rhodobacter capsulatus DE442 gene transfer agent baseplate

SupramoleculeName: Rhodobacter capsulatus DE442 gene transfer agent baseplate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: host recognition device present at the tip of the tail, empty particle
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
Molecular weightTheoretical: 1.00 MDa

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Macromolecule #1: Putative gene transfer agent protein

MacromoleculeName: Putative gene transfer agent protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MAYPESLKAH LQGGVTTLAR AWALARADGR VLGFTDHDVV LRFDGISFEP GSGMTAKAVL QGTGLSVDNT ESYGALSSEA ITEADLLAG RYDGAAVTVW LVNWADPAMR AVIFRGHLGE VSRGAGAFTA ELRGLTAALG QEQGRIYHPR CAAVLGDGRC R FDLTKDGY ...String:
MAYPESLKAH LQGGVTTLAR AWALARADGR VLGFTDHDVV LRFDGISFEP GSGMTAKAVL QGTGLSVDNT ESYGALSSEA ITEADLLAG RYDGAAVTVW LVNWADPAMR AVIFRGHLGE VSRGAGAFTA ELRGLTAALG QEQGRIYHPR CAAVLGDGRC R FDLTKDGY ALEAALGGVD EAVVLRLAEG AGFEDRWFEK GRLVVLDGAA AGLIGVVKND RLQADGSRLI ELWQRLGANP VA GDRVRIE PGCDKRAGTC RLKFDNFLNF RGFPHIPGED WMVSYPVQSG TNDGGSLFR

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Macromolecule #2: Putative gene transfer agent protein

MacromoleculeName: Putative gene transfer agent protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString: MATILLSAAG AAIGGGFGGT VLGLSGAVIG RAVGATLGRV IDQRLLGSGS QSVETGRVDR LRLSSASEGE AVGRLWGRMR VAGQVIWAT RFFESASVEK SGKGVPRATV TSYSYSLSLA LALCEGEILR VGRVWADGSE IEVSGLNMRV YRGGEDQLPD P KIAAVEGA ...String:
MATILLSAAG AAIGGGFGGT VLGLSGAVIG RAVGATLGRV IDQRLLGSGS QSVETGRVDR LRLSSASEGE AVGRLWGRMR VAGQVIWAT RFFESASVEK SGKGVPRATV TSYSYSLSLA LALCEGEILR VGRVWADGSE IEVSGLNMRV YRGGEDQLPD P KIAAVEGA EAAPAYRGIA YVVLEDLQLA PFGNRVPQFT FEVVRAAQGA LAEAEPDLTR GLRAVALIPG TGEYALATTP VY LATGSGV TATQGVANQN APGGQTDLVA ALERLDEELP NCGAVSLVVS WFGDDLRCGA CDVKPKVASV AEEGANMPWR VAG LERAGA EEVPRLSGQS VYGGTPADAA VIEAIAALRA AGKAVTFYPF ILMAQLAGNG LPDPWNPGSA QPALPWRGRI TLSV APGRA GSPDGTAAAE AQVAGFFGAA SPGDSAIAGG EVVYSGPEEW SMRRFILHYA HLCQLAGGVD AFCIGTEMVA LTQIR GPSN SFPAVAAFRQ LAGEVKAILG PGCKIGYAAD WSEYWGYAPG NGERFFHLDP LWADENIDFI GIDNYLPLSD WRDGAD HAD AGWGSIHALD YLRSNIEGGE YYDWFYAAPE HRAAQIRTPI TDGDHDEPWI WRAKDLRNWW LNDHHERVGG LRSEVAT AW VPQSKPIWFT EMGCAAIDKG TNQPNKFLDP KSSESGLPHH SDGRRDELIQ MQYLRAMTGY WGEAARNPVS AVYGGPML D MSRAHVWAWD ARPWPQFPLN TALWSDGENY ARGHWISGRA VAQPLASVVA EICGAAGITE IDVSGLYGLV RGYTMTGDQ TGRAGLQALM LAYGFEALER DGQLVFRMRD GRVAADLAAA DLALGEGEAV VETVRAAEAE IAGRVRLAYV EAEGDFEVKA VEAVFPDAA AGAAAGSELS LALTRAQAQG IVGRWLAEAR VARDTARFAL PPSRGHLGTG DVVRLDLPEG KRRYRIDRVE Q AGLIQVEA VRVEPGIYAP ADEVEDPASL RPFAAPVPVT AVFLDLPLMK GDEDPVAPHL AVTATPWPGT VAVWSSDEDA GY ALNASLG TRAVIGQTLT PLFRARPGVW DRGAALRVRL ASGALDSATA AKVLNGANAM AIGDGSSENW EVFQFAEAAL VEG KIWDIS LRLRGQLGTD ALMPEVWPEG SVVVALNGAP EQILLPSAAR GLARHYRIGA AVRSYDDPSF VHRIEAFAGA GLRP FSPCH LRAEPGASGW AFRWVRRTRI DGDSWQGYEV PLGETAELYL VRVLEGTAVK REVTVGEASW SYPAALQAAD GIAGA FTLE VAQVSDVYGP GLAARITVGA

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Macromolecule #3: Putative gene transfer agent protein

MacromoleculeName: Putative gene transfer agent protein / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
SequenceString: MAFHEVRFPA NLSFGSVGGP ERRTEIVTLS SGHEERNSPW AHSRRHYDAG VGLRSLDDVE RLIAFFEARG GQLHGFRWKD WADFKSCPA SRAVAHEDQL IGMGDGVTTA FQLVKTYVSG GQSYLRPIVK PVEGTVKLGI AGDHQAEAVN FAVDHATGIV S FNEPPPQG ...String:
MAFHEVRFPA NLSFGSVGGP ERRTEIVTLS SGHEERNSPW AHSRRHYDAG VGLRSLDDVE RLIAFFEARG GQLHGFRWKD WADFKSCPA SRAVAHEDQL IGMGDGVTTA FQLVKTYVSG GQSYLRPIVK PVEGTVKLGI AGDHQAEAVN FAVDHATGIV S FNEPPPQG ARVTAGFEFD VPVRFDTDRI AVSVQSFQAG DLPQVPVVEV RI

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Macromolecule #4: Tail fiber protein Rcc00171

MacromoleculeName: Tail fiber protein Rcc00171 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
SequenceString: MADQTPLLGL PLILPSQAQK HVTHNEALSL LDAIVQLAVL DRVRTAPPAS PQTGDRHIVA PGGAAAWTGQ DGAVALWTGS GWLFAQPQPG WTARDLSDGA LLIFDGSLWG PAPVATDNLP GLGINTTHDT TNRLAVQAAA TLLSHAGAGH QLKINKALPT DTASLLFQTS ...String:
MADQTPLLGL PLILPSQAQK HVTHNEALSL LDAIVQLAVL DRVRTAPPAS PQTGDRHIVA PGGAAAWTGQ DGAVALWTGS GWLFAQPQPG WTARDLSDGA LLIFDGSLWG PAPVATDNLP GLGINTTHDT TNRLAVQAAA TLLSHAGAGH QLKINKALPT DTASLLFQTS WSGRAEMGTT GSDSFAIKVS ADGTAWKTAF SFAGATGLAS GLAVQQSRTD VTAGRLMRAD WGYGPGNLLG TVAQSAGVPT GAVLERGTTA NGEYIRFADG TQICFAQRPL GSIIAQGAGS FAAPYRTADV SWTYPKVFSA APVVTCRGVA PVGLTQDRRL CAGGVGDLDA TAATGIHVVR LGGAANADVF KADLIAIGPW V

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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 mMNaClSodium chloride
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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 56954
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
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 2 / Software - Name: RELION (ver. 2.1)
Details: 2D classification for discarding particles without/with damaged baseplate followed by 3D classification, separating particles into two classes
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 26978
FSC plot (resolution estimation)

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