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Yorodumi- EMDB-5528: Cryo-EM structure of the contracted bacteriophage T4 tail contain... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5528 | |||||||||
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Title | Cryo-EM structure of the contracted bacteriophage T4 tail containing the collar and whiskers made of fibritin molecules. | |||||||||
Map data | Cryo-EM reconstruction of the contracted T4 tail containing the collar and whiskers | |||||||||
Sample |
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Keywords | bacteriophage / T4 / phage / collar / whiskers / fibritin | |||||||||
Function / homology | Fibritin C-terminal / Fibritin C-terminal region / virion component / Fibritin Function and homology information | |||||||||
Biological species | Enterobacteria phage T4 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 25.0 Å | |||||||||
Authors | Fokine A / Zhang Z / Kanamaru S / Bowman VD / Aksyuk AA / Arisaka F / Rao VB / Rossmann MG | |||||||||
Citation | Journal: J Mol Biol / Year: 2013 Title: The molecular architecture of the bacteriophage T4 neck. Authors: Andrei Fokine / Zhihong Zhang / Shuji Kanamaru / Valorie D Bowman / Anastasia A Aksyuk / Fumio Arisaka / Venigalla B Rao / Michael G Rossmann / Abstract: A hexamer of the bacteriophage T4 tail terminator protein, gp15, attaches to the top of the phage tail stabilizing the contractile sheath and forming the interface for binding of the independently ...A hexamer of the bacteriophage T4 tail terminator protein, gp15, attaches to the top of the phage tail stabilizing the contractile sheath and forming the interface for binding of the independently assembled head. Here we report the crystal structure of the gp15 hexamer, describe its interactions in T4 virions that have either an extended tail or a contracted tail, and discuss its structural relationship to other phage proteins. The neck of T4 virions is decorated by the "collar" and "whiskers", made of fibritin molecules. Fibritin acts as a chaperone helping to attach the long tail fibers to the virus during the assembly process. The collar and whiskers are environment-sensing devices, regulating the retraction of the long tail fibers under unfavorable conditions, thus preventing infection. Cryo-electron microscopy analysis suggests that twelve fibritin molecules attach to the phage neck with six molecules forming the collar and six molecules forming the whiskers. | |||||||||
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_5528.map.gz | 26 MB | EMDB map data format | |
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Header (meta data) | emd-5528-v30.xml emd-5528.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | emd_5528_1.jpg | 73.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5528 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5528 | HTTPS FTP |
-Validation report
Summary document | emd_5528_validation.pdf.gz | 376.8 KB | Display | EMDB validaton report |
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Full document | emd_5528_full_validation.pdf.gz | 376.3 KB | Display | |
Data in XML | emd_5528_validation.xml.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5528 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5528 | HTTPS FTP |
-Related structure data
Related structure data | 3j2oMC 3j2mC 3j2nC 4hudC 4huhC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5528.map.gz / Format: CCP4 / Size: 58.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM reconstruction of the contracted T4 tail containing the collar and whiskers | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.572 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 : bacteriophage T4
Entire | Name: bacteriophage T4 (virus) |
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Components |
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-Supramolecule #1000: bacteriophage T4
Supramolecule | Name: bacteriophage T4 / type: sample / ID: 1000 / Details: The phage tails were contracted using 4M urea. / Number unique components: 1 |
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-Supramolecule #1: Enterobacteria phage T4
Supramolecule | Name: Enterobacteria phage T4 / type: virus / ID: 1 / Name.synonym: Enterobacteria phage T4 / NCBI-ID: 10665 / Sci species name: Enterobacteria phage T4 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Enterobacteria phage T4 |
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Host (natural) | Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 / Details: 50 mM Tris-HCl, pH 8.0, 0.2 M NaCl, 8 mM MgCl2 |
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Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Date | Mar 7, 2007 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 97 / Average electron dose: 16 e/Å2 / Bits/pixel: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 39190 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 38000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: phase flipping |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN Details: The reconstruction of the contracted T4 tail which lacked the collar and whiskers (EMDB accession code 1086; Leiman et al., 2004, Cell 118, 419-429) was used as the initial model. Number images used: 2727 |