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- PDB-6tb9: Capsid of native GTA particle computed with C5 symmetry -

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Basic information

Entry
Database: PDB / ID: 6tb9
TitleCapsid of native GTA particle computed with C5 symmetry
Components
  • Head spike base Rcc01079
  • Head spike fiber Rcc01080
  • Major capsid protein Rcc01687
KeywordsVIRUS / "capsid" / "gene transfer agent" / "bacteriophage" / "HK97"
Function / homologyPhage capsid / Phage capsid family / : / : / Phage major capsid protein, HK97 family
Function and homology information
Biological speciesRhodobacter capsulatus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 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
DepositionNov 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / 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_assembly.details / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Movie
  • Biological unit as author_defined_assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-10442
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-10442
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C5: Major capsid protein Rcc01687
X4: Major capsid protein Rcc01687
Y4: Major capsid protein Rcc01687
Z4: Major capsid protein Rcc01687
A5: Major capsid protein Rcc01687
B5: Major capsid protein Rcc01687
N4: Major capsid protein Rcc01687
R4: Major capsid protein Rcc01687
M4: Major capsid protein Rcc01687
Q4: Major capsid protein Rcc01687
O4: Major capsid protein Rcc01687
P4: Major capsid protein Rcc01687
W4: Major capsid protein Rcc01687
U4: Major capsid protein Rcc01687
T4: Major capsid protein Rcc01687
S4: Major capsid protein Rcc01687
K4: Major capsid protein Rcc01687
J4: Major capsid protein Rcc01687
V4: Major capsid protein Rcc01687
L4: Major capsid protein Rcc01687
H4: Major capsid protein Rcc01687
I4: Major capsid protein Rcc01687
A4: Major capsid protein Rcc01687
D4: Major capsid protein Rcc01687
E4: Major capsid protein Rcc01687
F4: Major capsid protein Rcc01687
G4: Major capsid protein Rcc01687
B4: Major capsid protein Rcc01687
C4: Major capsid protein Rcc01687
E3: Head spike base Rcc01079
D3: Head spike base Rcc01079
A3: Head spike base Rcc01079
C3: Head spike base Rcc01079
B3: Head spike base Rcc01079
F3: Head spike fiber Rcc01080
A1: Head spike base Rcc01079
E2: Head spike base Rcc01079
D2: Head spike base Rcc01079
A2: Head spike base Rcc01079
C2: Head spike base Rcc01079
B2: Head spike base Rcc01079
F2: Head spike fiber Rcc01080


Theoretical massNumber of molelcules
Total (without water)1,354,62142
Polymers1,354,62142
Non-polymers00
Water0
1
C5: Major capsid protein Rcc01687
X4: Major capsid protein Rcc01687
Y4: Major capsid protein Rcc01687
Z4: Major capsid protein Rcc01687
A5: Major capsid protein Rcc01687
B5: Major capsid protein Rcc01687
N4: Major capsid protein Rcc01687
R4: Major capsid protein Rcc01687
M4: Major capsid protein Rcc01687
Q4: Major capsid protein Rcc01687
O4: Major capsid protein Rcc01687
P4: Major capsid protein Rcc01687
W4: Major capsid protein Rcc01687
U4: Major capsid protein Rcc01687
T4: Major capsid protein Rcc01687
S4: Major capsid protein Rcc01687
K4: Major capsid protein Rcc01687
J4: Major capsid protein Rcc01687
V4: Major capsid protein Rcc01687
L4: Major capsid protein Rcc01687
H4: Major capsid protein Rcc01687
I4: Major capsid protein Rcc01687
A4: Major capsid protein Rcc01687
D4: Major capsid protein Rcc01687
E4: Major capsid protein Rcc01687
F4: Major capsid protein Rcc01687
G4: Major capsid protein Rcc01687
B4: Major capsid protein Rcc01687
C4: Major capsid protein Rcc01687
E3: Head spike base Rcc01079
D3: Head spike base Rcc01079
A3: Head spike base Rcc01079
C3: Head spike base Rcc01079
B3: Head spike base Rcc01079
F3: Head spike fiber Rcc01080
A1: Head spike base Rcc01079
E2: Head spike base Rcc01079
D2: Head spike base Rcc01079
A2: Head spike base Rcc01079
C2: Head spike base Rcc01079
B2: Head spike base Rcc01079
F2: Head spike fiber Rcc01080
x 5


Theoretical massNumber of molelcules
Total (without water)6,773,107210
Polymers6,773,107210
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4

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Components

#1: Protein ...
Major capsid protein Rcc01687


Mass: 40982.066 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus (bacteria) / References: UniProt: D5ATZ3
#2: Protein
Head spike base Rcc01079


Mass: 9104.348 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus (bacteria) / References: UniProt: A0A507Z9H3
#3: Protein Head spike fiber Rcc01080


Mass: 32996.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus (bacteria) / References: UniProt: A0A507Z6Q1

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Rhodobacter capsulatus DE442 gene transfer agent capsidCOMPLEXOblate T=3 capsid (without portal) decorated with head spikes, native particleall0NATURAL
2Head spikeCOMPLEXprotrusion of the capsid on 5-fold vertices, composed out of base pentamer and fiber monomer#2-#31NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
115.42 MDaNO
210.08 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
11Rhodobacter capsulatus (bacteria)1061Gene transfer agent
22Rhodobacter capsulatus (bacteria)1061Gene transfer agent
Details of virus
IDEntity assembly-IDEmptyEnvelopedIsolateType
11NONOSTRAINVIRION
22
Natural host
IDEntity assembly-IDOrganismNcbi tax-ID
11Rhodobacter capsulatus1061
12
Virus shell
IDEntity assembly-IDNameDiameter (nm)Triangulation number (T number)
11HK97-like oblate capsid3803
12
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
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 %

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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

EM software
IDNameVersionCategory
1RELION2.1particle selection
2EPU2.1image acquisition
4RELION2.1CTF correction
7Coot0.9model fitting
9RELION2.1initial Euler assignment
10RELION3final Euler assignment
12RELION33D reconstruction
19PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 53432
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39403 / Algorithm: BACK PROJECTION / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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