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- PDB-6to8: Neck of empty GTA particle computed with C12 symmetry -

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Basic information

Entry
Database: PDB / ID: 6to8
TitleNeck of empty GTA particle computed with C12 symmetry
Components
  • Adaptor protein Rcc01688
  • Portal protein Rcc01684
KeywordsVIRUS / "adaptor" / "connector" / "neck" / "portal"
Function / homologyPhage conserved hypothetical protein / Phage portal protein, HK97 / Bacteriophage/Gene transfer agent portal protein / Phage portal protein / Phage portal protein, HK97 family / Gene transfer agent protein
Function and homology information
Biological speciesRhodobacter capsulatus DE442 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 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 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

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Assembly

Deposited unit
B: Adaptor protein Rcc01688
A: Portal protein Rcc01684


Theoretical massNumber of molelcules
Total (without water)63,8032
Polymers63,8032
Non-polymers00
Water00
1
B: Adaptor protein Rcc01688
A: Portal protein Rcc01684
x 12


Theoretical massNumber of molelcules
Total (without water)765,63924
Polymers765,63924
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation11

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Components

#1: Protein Adaptor protein Rcc01688


Mass: 20956.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus DE442 (bacteria) / References: UniProt: D5ATZ4
#2: Protein Portal protein Rcc01684


Mass: 42846.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus DE442 (bacteria) / References: UniProt: D5ATZ0

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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 connector
Type: COMPLEX
Details: special 5-fold vertex of the capsid, interconnecting capsid to tail
Entity ID: all / Source: NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.76 MDaNO
210.76 MDaNO
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
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 mMNaCl1
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
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
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 FIELD / Nominal magnification: 75000 X / 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: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
1RELION2.1particle selection
2EPU2.1image acquisition
4RELION2.1CTF correction
7Coot0.9model fitting
9RELION2.1initial Euler assignment
10RELION3final Euler assignment
11RELION2.1classification
12RELION33D reconstruction
13PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 49821
SymmetryPoint symmetry: C12 (12 fold cyclic)
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35512 / Algorithm: BACK PROJECTION / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d
ELECTRON MICROSCOPYf_angle_d1.13369222
ELECTRON MICROSCOPYf_dihedral_angle_d15.78430210
ELECTRON MICROSCOPYf_chiral_restr0.0647680
ELECTRON MICROSCOPYf_plane_restr0.0099042

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