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- PDB-6tsw: Isometric capsid of empty GTA particle computed with I4(I,n25r) s... -

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Entry
Database: PDB / ID: 6tsw
TitleIsometric capsid of empty GTA particle computed with I4(I,n25r) symmetry
ComponentsMajor capsid protein Rcc01687
KeywordsVIRUS / "capsid" / "mutant" / "variant" / "HK97"
Function / homologyPhage capsid / Phage capsid family / Phage major capsid protein, HK97 family
Function and homology information
Biological speciesRhodobacter capsulatus DE442 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.03 Å
AuthorsBardy, P. / Fuzik, T. / Hrebik, D. / Pantucek, R. / Beatty, J.T. / Plevka, P.
Funding support Czech Republic, 7items
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, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release

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  • Simplified surface model + fitted atomic model
  • EMDB-10567
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Assembly

Deposited unit
B: Major capsid protein Rcc01687
C: Major capsid protein Rcc01687
A: Major capsid protein Rcc01687


Theoretical massNumber of molelcules
Total (without water)122,9463
Polymers122,9463
Non-polymers00
Water0
1
B: Major capsid protein Rcc01687
C: Major capsid protein Rcc01687
A: Major capsid protein Rcc01687
x 60


Theoretical massNumber of molelcules
Total (without water)7,376,772180
Polymers7,376,772180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1
point symmetry operation59

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Components

#1: Protein Major capsid protein Rcc01687


Mass: 40982.066 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus DE442 (bacteria) / References: UniProt: D5ATZ3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Rhodobacter capsulatus DE442 gene transfer agent capsid
Type: COMPLEX
Details: T=3 isometric capsid of GTA particle, population variant. One percent of observed particles contained this assembly.
Entity ID: all / Source: NATURAL
Molecular weight
IDEntity assembly-IDUnitsExperimental value
11NO
21MEGADALTONSYES
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria) / Strain: Gene transfer agent
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Rhodobacter capsulatus
Virus shellName: HK97-like capsid / Diameter: 380 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.8 / Details: G-buffer, doi: 10.1016/0003-9861(77)90508-2
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTris1
21 mMNaClSodium chloride1
31 mMMgCl21
41 mMCaCl21
50.01 mg/mlBovine serum albumin1
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: -3000 nm / Nominal defocus min: -1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 42.75 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3114
Image scansWidth: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategory
1RELION2.1particle selection
2EPU2.1image acquisition
4RELION2.1CTF correction
7Coot0.9model fitting
9PHENIX1.16model refinement
10RELION2.1initial Euler assignment
11RELION3final Euler assignment
12RELION2.1classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1076
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 898 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007100830
ELECTRON MICROSCOPYf_angle_d0.79137100
ELECTRON MICROSCOPYf_dihedral_angle_d15.97359700
ELECTRON MICROSCOPYf_chiral_restr0.04715615
ELECTRON MICROSCOPYf_plane_restr0.00617880

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