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Yorodumi- EMDB-3396: Cryo-electron microscopy structure of the star-shaped, hubless po... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3396 | |||||||||
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Title | Cryo-electron microscopy structure of the star-shaped, hubless post-attachment T4 baseplate | |||||||||
Map data | Cryo-electron microscopy structure of the star-shaped, hubless post-attachment T4 baseplate. Postprocessed with Relion, using automated B-factor estimation and the mask used for polishing, which was generated previously by auto-masking with an initial binarization threshold of 0.015. | |||||||||
Sample |
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Keywords | T4 / baseplate / post-attachment / bacteriophage / bacterial virus / star-shaped / hubless / membrane-piercing / cell attachment / infection | |||||||||
Function / homology | Function and homology information virus tail, baseplate / viral tail assembly / viral release from host cell / identical protein binding Similarity search - Function | |||||||||
Biological species | Enterobacteria phage T4 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.77 Å | |||||||||
Authors | Taylor NMI / Guerrero-Ferreira RC / Goldie KN / Stahlberg H / Leiman PG | |||||||||
Citation | Journal: Nature / Year: 2016 Title: Structure of the T4 baseplate and its function in triggering sheath contraction. Authors: Nicholas M I Taylor / Nikolai S Prokhorov / Ricardo C Guerrero-Ferreira / Mikhail M Shneider / Christopher Browning / Kenneth N Goldie / Henning Stahlberg / Petr G Leiman / Abstract: Several systems, including contractile tail bacteriophages, the type VI secretion system and R-type pyocins, use a multiprotein tubular apparatus to attach to and penetrate host cell membranes. This ...Several systems, including contractile tail bacteriophages, the type VI secretion system and R-type pyocins, use a multiprotein tubular apparatus to attach to and penetrate host cell membranes. This macromolecular machine resembles a stretched, coiled spring (or sheath) wound around a rigid tube with a spike-shaped protein at its tip. A baseplate structure, which is arguably the most complex part of this assembly, relays the contraction signal to the sheath. Here we present the atomic structure of the approximately 6-megadalton bacteriophage T4 baseplate in its pre- and post-host attachment states and explain the events that lead to sheath contraction in atomic detail. We establish the identity and function of a minimal set of components that is conserved in all contractile injection systems and show that the triggering mechanism is universally conserved. | |||||||||
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_3396.map.gz | 28.3 MB | EMDB map data format | |
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Header (meta data) | emd-3396-v30.xml emd-3396.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3396_fsc.xml | 16.5 KB | Display | FSC data file |
Images | emd_3396.png | 99.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3396 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3396 | HTTPS FTP |
-Validation report
Summary document | emd_3396_validation.pdf.gz | 258.5 KB | Display | EMDB validaton report |
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Full document | emd_3396_full_validation.pdf.gz | 257.6 KB | Display | |
Data in XML | emd_3396_validation.xml.gz | 15.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3396 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3396 | HTTPS FTP |
-Related structure data
Related structure data | 5iv7MC 3374C 3392C 3393C 3394C 3395C 3397C 5iv5C 5iw9C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3396.map.gz / Format: CCP4 / Size: 412 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-electron microscopy structure of the star-shaped, hubless post-attachment T4 baseplate. Postprocessed with Relion, using automated B-factor estimation and the mask used for polishing, which was generated previously by auto-masking with an initial binarization threshold of 0.015. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.326 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 : Star-shaped, hubless post-attachment T4 baseplate
Entire | Name: Star-shaped, hubless post-attachment T4 baseplate |
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Components |
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-Supramolecule #1000: Star-shaped, hubless post-attachment T4 baseplate
Supramolecule | Name: Star-shaped, hubless post-attachment T4 baseplate / type: sample / ID: 1000 Details: In addition to hexagonal pre-attachment baseplate-tail tube complexes, the sample also contained some star-shaped, hubless post-attachment baseplates. The current reconstruction is the ...Details: In addition to hexagonal pre-attachment baseplate-tail tube complexes, the sample also contained some star-shaped, hubless post-attachment baseplates. The current reconstruction is the reconstruction of those post-attachment, star-shaped baseplates, which have the following oligomeric state: (gp6)12(gp7)6(gp8)12(gp9)18(gp10)18(gp11)18(gp12)18(gp25)6(gp53)6. This oligomeric state has an approximate theoretical MW of 5.5 MDa. Oligomeric state: (gp6)12(gp7)6(gp8)12(gp9)18(gp10)18(gp11)18(gp12)18(gp25)6(gp53)6 Number unique components: 1 |
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Molecular weight | Theoretical: 5.5 MDa |
-Macromolecule #1: Star-shaped, hubless post-attachment T4 baseplate
Macromolecule | Name: Star-shaped, hubless post-attachment T4 baseplate / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: Enterobacteria phage T4 (virus) / Strain: am18/am23 mutant |
Molecular weight | Theoretical: 8.7 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 / Details: 50 mM Tris-HCl pH 8.0, 100 mM NaCl, 8 mM MgSO4 |
Grid | Details: Quantifoil 300 mesh carbon-coated copper grids glow-discharged for 20 seconds |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV Method: Applied 3.5 ul of sample and blotting 3 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Average: 80 K |
Alignment procedure | Legacy - Astigmatism: The astigmatism was corrected at high magnification |
Specialist optics | Energy filter - Name: Quantum-LS Gatan Image Filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | May 7, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 1621 / Average electron dose: 60 e/Å2 Details: Individual frames were aligned with 2dx_automator. 40 frames were recorded in total, and the 2 first frames were discarded. Bits/pixel: 32 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 37700 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |