+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10541 | ||||||||||||||||||||||||
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Title | Neck of empty GTA particle computed with C12 symmetry | ||||||||||||||||||||||||
Map data | neck of empty GTA particle, C12 symmetry region | ||||||||||||||||||||||||
Sample |
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Keywords | "adaptor" / "connector" / "neck" / "portal" / VIRUS | ||||||||||||||||||||||||
Function / homology | Phage 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 species | Rhodobacter capsulatus DE442 (bacteria) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.36 Å | ||||||||||||||||||||||||
Authors | Bardy P / Fuzik T | ||||||||||||||||||||||||
Funding support | Czech Republic, 7 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10541.map.gz | 11.9 MB | EMDB map data format | |
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Header (meta data) | emd-10541-v30.xml emd-10541.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10541_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_10541.png | 196.6 KB | ||
Filedesc metadata | emd-10541.cif.gz | 6.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10541 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10541 | HTTPS FTP |
-Validation report
Summary document | emd_10541_validation.pdf.gz | 455.6 KB | Display | EMDB validaton report |
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Full document | emd_10541_full_validation.pdf.gz | 455.2 KB | Display | |
Data in XML | emd_10541_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | emd_10541_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10541 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10541 | HTTPS FTP |
-Related structure data
Related structure data | 6to8MC 6tb9C 6tbaC 6te8C 6te9C 6teaC 6tebC 6tehC 6toaC 6tsuC 6tsvC 6tswC 6tuiC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10541.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | neck of empty GTA particle, C12 symmetry region | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : Rhodobacter capsulatus DE442 gene transfer agent connector
Entire | Name: Rhodobacter capsulatus DE442 gene transfer agent connector |
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Components |
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-Supramolecule #1: Rhodobacter capsulatus DE442 gene transfer agent connector
Supramolecule | Name: Rhodobacter capsulatus DE442 gene transfer agent connector type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: special 5-fold vertex of the capsid, interconnecting capsid to tail |
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Source (natural) | Organism: Rhodobacter capsulatus DE442 (bacteria) |
Molecular weight | Theoretical: 760 KDa |
-Macromolecule #1: Adaptor protein Rcc01688
Macromolecule | Name: Adaptor protein Rcc01688 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rhodobacter capsulatus DE442 (bacteria) |
Molecular weight | Theoretical: 20.956354 KDa |
Sequence | String: MMLNEVTAVP GTALPVAEFR DHLRLGTGFA DLGAEDAALL SYLRAAIAAI EGRTAKALIS RGFRLALTAW RWGDMQTLPI APVATVTAL RLVDAAGVET PVAAGWRLVP DMARPRIEAL GAMLPMIPTG GRVEIDFTAG FGASWSALPV DLAQAVFLLA A QYYELRHD ...String: MMLNEVTAVP GTALPVAEFR DHLRLGTGFA DLGAEDAALL SYLRAAIAAI EGRTAKALIS RGFRLALTAW RWGDMQTLPI APVATVTAL RLVDAAGVET PVAAGWRLVP DMARPRIEAL GAMLPMIPTG GRVEIDFTAG FGASWSALPV DLAQAVFLLA A QYYELRHD GAAEGGAMPF GVMALIERWR TVRVLGGRP UniProtKB: Gene transfer agent protein |
-Macromolecule #2: Portal protein Rcc01684
Macromolecule | Name: Portal protein Rcc01684 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rhodobacter capsulatus DE442 (bacteria) |
Molecular weight | Theoretical: 42.84691 KDa |
Sequence | String: MGLNFFRKAA PEVRTEPVAE RKASVTGRIV AMASGAGRPV WGPRDTVSLM RTGFAGNPVG FRSVKLIAEA TAAVPLICQD AERRYEIHP VLDLLRRPNA GQGRAELFEA LIGQILLSGN GYLEAVCPEP GVPRELHVLR SDRMAVVPGA DGWPVGYDYT V GGRKHRFD ...String: MGLNFFRKAA PEVRTEPVAE RKASVTGRIV AMASGAGRPV WGPRDTVSLM RTGFAGNPVG FRSVKLIAEA TAAVPLICQD AERRYEIHP VLDLLRRPNA GQGRAELFEA LIGQILLSGN GYLEAVCPEP GVPRELHVLR SDRMAVVPGA DGWPVGYDYT V GGRKHRFD MTGHPDPICH IKSFHPTDDH YGLSPMQAAA VALDVHNAAS AWSKALLDNA ARPSGAIIYK GADGQGVLAP EQ YERLIFE METHHQGARN AGRPMLLEGG LDWKPMGFSP SDMEFHETKA AAAREIALAF GVPPMLIGIP GDATYANYAE ANR AFYRLT VLPLLTRVSA ALAWWLSGYL GAQIELKPDL DQVPALAVER DQLWARIGAA GFLSNSEKRV LLGLPPTAEG UniProtKB: Phage portal protein, HK97 family |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-6to8: |