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Yorodumi- EMDB-5783: Bacteriophage-encoded Tubulin Homologue PhuZ Forms a Three-Strand... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5783 | |||||||||
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Title | Bacteriophage-encoded Tubulin Homologue PhuZ Forms a Three-Stranded Filament | |||||||||
Map data | Reconstruction of PhuZ filament structure | |||||||||
Sample |
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Keywords | PhuZ / FtsZ/tubulin-related protein / filament / helical reconstruction / Pseudomonas bacteriophages / 201phi2-1 | |||||||||
Function / homology | establishment of localization / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / host cell cytoplasm / GTPase activity / GTP binding / identical protein binding / Phage tubulin-like protein Function and homology information | |||||||||
Biological species | Pseudomonas phage 201phi2-1 (virus) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 7.1 Å | |||||||||
Authors | Zehr EA / Kraemer JA / Erb ML / Coker JKC / Montabana EA / Pogliano J / Agard DA | |||||||||
Citation | Journal: Structure / Year: 2014 Title: The structure and assembly mechanism of a novel three-stranded tubulin filament that centers phage DNA. Authors: Elena A Zehr / James A Kraemer / Marcella L Erb / Joanna K C Coker / Elizabeth A Montabana / Joe Pogliano / David A Agard / Abstract: Tubulins are a universally conserved protein superfamily that carry out diverse biological roles by assembling filaments with very different architectures. The underlying basis of this structural ...Tubulins are a universally conserved protein superfamily that carry out diverse biological roles by assembling filaments with very different architectures. The underlying basis of this structural diversity is poorly understood. Here, we determine a 7.1 Å cryo-electron microscopy reconstruction of the bacteriophage-encoded PhuZ filament and provide molecular-level insight into its cooperative assembly mechanism. The PhuZ family of tubulins is required to actively center the phage within infected host cells, facilitating efficient phage replication. Our reconstruction and derived model reveal the first example of a three-stranded tubulin filament. We show that the elongated C-terminal tail simultaneously stabilizes both longitudinal and lateral interactions, which in turn define filament architecture. Identified interaction surfaces are conserved within the PhuZ family, and their mutagenesis compromises polymerization in vitro and in vivo. Combining kinetic modeling of PhuZ filament assembly and structural data, we suggest a common filament structure and assembly mechanism for the PhuZ family of tubulins. | |||||||||
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_5783.map.gz | 28.5 MB | EMDB map data format | |
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Header (meta data) | emd-5783-v30.xml emd-5783.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | 400_5783.gif 80_5783.gif | 75.5 KB 5.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5783 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5783 | HTTPS FTP |
-Validation report
Summary document | emd_5783_validation.pdf.gz | 344 KB | Display | EMDB validaton report |
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Full document | emd_5783_full_validation.pdf.gz | 343.5 KB | Display | |
Data in XML | emd_5783_validation.xml.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5783 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5783 | HTTPS FTP |
-Related structure data
Related structure data | 3j5vMC 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_5783.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of PhuZ filament structure | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.20398 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 : PhuZ201 filament
Entire | Name: PhuZ201 filament |
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Components |
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-Supramolecule #1000: PhuZ201 filament
Supramolecule | Name: PhuZ201 filament / type: sample / ID: 1000 / Oligomeric state: filament / Number unique components: 1 |
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-Macromolecule #1: PhuZ
Macromolecule | Name: PhuZ / type: protein_or_peptide / ID: 1 / Name.synonym: PhuZ201 / Oligomeric state: polymer / Recombinant expression: Yes |
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Source (natural) | Organism: Pseudomonas phage 201phi2-1 (virus) / synonym: bacteriophage |
Molecular weight | Experimental: 34.621 KDa / Theoretical: 34.621 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET28a(+) |
Sequence | UniProtKB: Phage tubulin-like protein / InterPro: Tubulin/FtsZ, GTPase domain |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.7 mg/mL |
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Buffer | pH: 8 Details: 50 mM HEPES, 125 mM KCl, 5 mM MgCl2, 5% glycerol, 1 mM GMPCPP |
Grid | Details: C-FLAT holey carbon grid, 200 mesh copper grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK III Method: Sample was applied to C-FLAT holey carbon grids, blotted for 2 seconds, and flash frozen in liquid ethane |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Alignment procedure | Legacy - Astigmatism: Astigmatism corrected at 250,000 times magnification |
Date | Nov 21, 2011 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 461 / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 62000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | Reconstruction was determined by IHRSR. |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 14.4 Å Applied symmetry - Helical parameters - Δ&Phi: 116.4 ° Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: OTHER / Software - Name: Spider |
CTF correction | Details: Whole micrograph |