[English] 日本語
Yorodumi- EMDB-6323: CryoEM single particle reconstruction of prolate head of bacterio... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6323 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM single particle reconstruction of prolate head of bacteriophage T4 | |||||||||
Map data | Reconstruction of empty T4 prolate head | |||||||||
Sample |
| |||||||||
Keywords | T4 prolate head | |||||||||
Biological species | Enterobacteria phage T4 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.0 Å | |||||||||
Authors | Sun L / Zhang X / Gao S / Rao PA / Padilla-Sanchez V / Chen Z / Sun S / Xiang Y / Rao VB / Rossmann MG | |||||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution. Authors: Lei Sun / Xinzheng Zhang / Song Gao / Prashant A Rao / Victor Padilla-Sanchez / Zhenguo Chen / Siyang Sun / Ye Xiang / Sriram Subramaniam / Venigalla B Rao / Michael G Rossmann / Abstract: The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage ...The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage T4 portal assembly, gene product 20 (gp20), determined by cryo-electron microscopy (cryo-EM) to 3.6 Å resolution. In addition, analysis of a 10 Å resolution cryo-EM map of an empty prolate T4 head shows how the dodecameric portal assembly interacts with the capsid protein gp23 at the special pentameric vertex. The gp20 structure also verifies that the portal assembly is required for initiating head assembly, for attachment of the packaging motor, and for participation in DNA packaging. Comparison of the Myoviridae T4 portal structure with the known portal structures of φ29, SPP1 and P22, representing Podo- and Siphoviridae, shows that the portal structure probably dates back to a time when self-replicating microorganisms were being established on Earth. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6323.map.gz | 124.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6323-v30.xml emd-6323.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | 400_6323.gif 80_6323.gif | 114.5 KB 5.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6323 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6323 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_6323.map.gz / Format: CCP4 / Size: 976.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of empty T4 prolate head | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : empty T4 prolate head
Entire | Name: empty T4 prolate head |
---|---|
Components |
|
-Supramolecule #1000: empty T4 prolate head
Supramolecule | Name: empty T4 prolate head / type: sample / ID: 1000 / Number unique components: 1 |
---|---|
Molecular weight | Theoretical: 82 MDa |
-Supramolecule #1: Enterobacteria phage T4
Supramolecule | Name: Enterobacteria phage T4 / type: virus / ID: 1 / Details: empty head / NCBI-ID: 10665 / Sci species name: Enterobacteria phage T4 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes |
---|---|
Host (natural) | Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA) |
Molecular weight | Theoretical: 82 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
---|---|
Buffer | pH: 7.5 / Details: 50 mM Tris, 1 mM MgCl2, 100 mM NaCl |
Grid | Details: 400 mesh copper grid with thin holey carbon film, glow discharged in amylamine atmosphere |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 5 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 60521 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000 |
Specialist optics | Energy filter - Name: Gatan / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 25.0 eV |
Sample stage | Specimen holder: Liquid nitrogen-cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Temperature | Min: 80 K / Max: 105 K / Average: 100 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 250,000 times magnification. |
Date | Aug 9, 2013 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 473 / Average electron dose: 22.0 e/Å2 / Bits/pixel: 8 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each particle |
---|---|
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 13000 |
Details | The particles were selected using an automatic selection program. |