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- EMDB-10565: Capsid of empty GTA particle computed with C5 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-10565
TitleCapsid of empty GTA particle computed with C5 symmetry
Map datacapsid of empty GTA particle, C5 symmetry
Sample
  • Complex: Rhodobacter capsulatus DE442 gene transfer agent capsid
    • Complex: Head spike
      • Protein or peptide: Uncharacterized protein
      • Protein or peptide: Uncharacterized protein
    • Protein or peptide: Major capsid protein Rcc01687
Keywords"capsid" / "jelly roll" / "spike" / "HK97" / VIRUS
Function / homologyPhage capsid / Phage capsid family / Uncharacterized protein / Uncharacterized protein / Phage major capsid protein, HK97 family
Function and homology information
Biological speciesRhodobacter capsulatus DE442 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 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 21, 2019-
Header (metadata) releaseFeb 16, 2022-
Map releaseFeb 16, 2022-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.113
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.113
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tsu
  • Surface level: 0.113
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6tsu
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10565.png

Downloads & links

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Map

FileDownload / File: emd_10565.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcapsid of empty GTA particle, C5 symmetry
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: 0.113 / Movie #1: 0.113
Minimum - Maximum-0.3406905 - 0.5602565
Average (Standard dev.)0.0019961165 (±0.023792475)
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-0.3410.5600.002

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Supplemental data

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Sample components

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Entire : Rhodobacter capsulatus DE442 gene transfer agent capsid

EntireName: Rhodobacter capsulatus DE442 gene transfer agent capsid
Components
  • Complex: Rhodobacter capsulatus DE442 gene transfer agent capsid
    • Complex: Head spike
      • Protein or peptide: Uncharacterized protein
      • Protein or peptide: Uncharacterized protein
    • Protein or peptide: Major capsid protein Rcc01687

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Supramolecule #1: Rhodobacter capsulatus DE442 gene transfer agent capsid

SupramoleculeName: Rhodobacter capsulatus DE442 gene transfer agent capsid
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Oblate T=3 capsid (without portal) decorated with head spikes, empty particle
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
Molecular weightTheoretical: 80 KDa

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Supramolecule #2: Head spike

SupramoleculeName: Head spike / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Details: protrusion of the capsid on 5-fold vertices, composed out of base pentamer and fiber monomer
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)

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Macromolecule #1: Major capsid protein Rcc01687

MacromoleculeName: Major capsid protein Rcc01687 / type: protein_or_peptide / ID: 1 / Number of copies: 29 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
Molecular weightTheoretical: 40.982066 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 AIKLLKFAAS

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 DE442 (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 DE442 (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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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: 85271
Startup modelType of model: INSILICO MODEL
In silico model: stochastic gradient descent in RELION 2.1 de novo
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 47071
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 2.1) / Details: several rounds of 2d classification preceded
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6tsu:
Capsid of empty GTA particle computed with C5 symmetry

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