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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10565 | ||||||||||||||||||||||||
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Title | Capsid of empty GTA particle computed with C5 symmetry | ||||||||||||||||||||||||
![]() | capsid of empty GTA particle, C5 symmetry | ||||||||||||||||||||||||
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Function / homology | Phage capsid / Phage capsid family / Uncharacterized protein / Uncharacterized protein / Phage major capsid protein, HK97 family![]() | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() | ||||||||||||||||||||||||
![]() | Bardy P / Fuzik T / Hrebik D / Pantucek R / Beatty JT / Plevka P | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 71.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.2 KB 20.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.1 KB | Display | ![]() |
Images | ![]() | 242.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tsuMC ![]() 6tb9C ![]() 6tbaC ![]() 6te8C ![]() 6te9C ![]() 6teaC ![]() 6tebC ![]() 6tehC ![]() 6to8C ![]() 6toaC ![]() 6tsvC ![]() 6tswC ![]() 6tuiC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | capsid of empty GTA particle, C5 symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.063 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Rhodobacter capsulatus DE442 gene transfer agent capsid
Entire | Name: Rhodobacter capsulatus DE442 gene transfer agent capsid |
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Components |
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-Supramolecule #1: Rhodobacter capsulatus DE442 gene transfer agent capsid
Supramolecule | Name: 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 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 80 KDa |
-Supramolecule #2: Head spike
Supramolecule | Name: 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 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Major capsid protein Rcc01687
Macromolecule | Name: Major capsid protein Rcc01687 / type: protein_or_peptide / ID: 1 / Number of copies: 29 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 40.982066 KDa |
Sequence | String: 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 |
-Macromolecule #2: Uncharacterized protein
Macromolecule | Name: Uncharacterized protein / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 9.104348 KDa |
Sequence | String: MDVFAKHAVS LESPAVRHYE ITPSDSTDLA RRPRALRVQT GGTLVLRDET GITVTYTVFA GEILPVRPVR VLATGTTATA VGWE |
-Macromolecule #3: Uncharacterized protein
Macromolecule | Name: Uncharacterized protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 32.996828 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 20 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.8 Component:
Details: G-buffer, doi: 10.1016/0003-9861(77)90508-2 | ||||||||||||||||||
Grid | Model: 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 | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film 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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-6tsu: |