[English] 日本語
![](img/lk-miru.gif)
- EMDB-1119: Three-dimensional structure of the bacteriophage P22 tail machine. -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-1119 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Three-dimensional structure of the bacteriophage P22 tail machine. | |||||||||
![]() | a cryoEM map of the P22 tail machine | |||||||||
![]() |
| |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 23.0 Å | |||||||||
![]() | Tang L / Marion WR / Cingolani G / Prevelige PE / Johnson JE | |||||||||
![]() | ![]() Title: Three-dimensional structure of the bacteriophage P22 tail machine. Authors: Liang Tang / William R Marion / Gino Cingolani / Peter E Prevelige / John E Johnson / ![]() Abstract: The tail of the bacteriophage P22 is composed of multiple protein components and integrates various biological functions that are crucial to the assembly and infection of the phage. The three- ...The tail of the bacteriophage P22 is composed of multiple protein components and integrates various biological functions that are crucial to the assembly and infection of the phage. The three-dimensional structure of the P22 tail machine determined by electron cryo-microscopy and image reconstruction reveals how the five types of polypeptides present as 51 subunits are organized into this molecular machine through twelve-, six- and three-fold symmetry, and provides insights into molecular events during host cell attachment and phage DNA translocation. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 1.4 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 13.8 KB 13.8 KB | Display Display | ![]() |
Images | ![]() | 23.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 214.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 213.8 KB | Display | |
Data in XML | ![]() | 5.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | a cryoEM map of the P22 tail machine | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : the tail machine isolated from bacteriophage P22
Entire | Name: the tail machine isolated from bacteriophage P22 |
---|---|
Components |
|
-Supramolecule #1000: the tail machine isolated from bacteriophage P22
Supramolecule | Name: the tail machine isolated from bacteriophage P22 / type: sample / ID: 1000 / Oligomeric state: 12-, 6-, and 3-fold symmetry / Number unique components: 5 |
---|---|
Molecular weight | Theoretical: 2.8 MDa |
-Macromolecule #1: portal
Macromolecule | Name: portal / type: protein_or_peptide / ID: 1 / Name.synonym: gp1 / Details: DNA packaging / Number of copies: 12 / Oligomeric state: dodecamer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 82.611 MDa / Theoretical: 83 MDa |
Recombinant expression | Organism: Salmonella enterica Serovar Typhimurium strain |
-Macromolecule #2: tailspike
Macromolecule | Name: tailspike / type: protein_or_peptide / ID: 2 / Name.synonym: gp9 / Details: receptor binding / Number of copies: 18 / Oligomeric state: trimer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 71.857 MDa / Theoretical: 70 MDa |
Recombinant expression | Organism: Salmonella enterica Serovar Typhimurium strain |
-Macromolecule #3: gp4
Macromolecule | Name: gp4 / type: protein_or_peptide / ID: 3 / Name.synonym: accessory protein / Details: forms a channel; transglycosylase / Number of copies: 12 / Oligomeric state: dodecamer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 18.025 MDa / Theoretical: 20 MDa |
Recombinant expression | Organism: Salmonella enterica Serovar Typhimurium strain |
-Macromolecule #4: gp10
Macromolecule | Name: gp10 / type: protein_or_peptide / ID: 4 / Name.synonym: accessory protein / Details: forms a channel / Number of copies: 6 / Oligomeric state: hexamer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 52.457 MDa / Theoretical: 50 MDa |
Recombinant expression | Organism: Salmonella enterica Serovar Typhimurium strain |
-Macromolecule #5: gp26
Macromolecule | Name: gp26 / type: protein_or_peptide / ID: 5 / Name.synonym: accessory protein / Details: needle-like plug / Number of copies: 3 / Oligomeric state: trimer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 24.603 MDa / Theoretical: 25 MDa |
Recombinant expression | Organism: Salmonella enterica Serovar Typhimurium strain |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 8 / Details: 50 mM Na2HPO4, pH8.0 |
---|---|
Grid | Details: 300 mesh holey copper grid |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 89 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home-made plunger / Method: blot for 3-4 seconds before plunging |
-
Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
---|---|
Temperature | Average: 89 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 105,000 times magnification |
Date | May 19, 2004 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 54 / Bits/pixel: 8 |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 60 |
-
Image processing
Details | The particles showed preferential orientation on the grids. CryoEM data were collected using the tilt method. The tilt angles ranged from 0-60 degrees. The particles were selected with a semi-automated selection program. |
---|---|
Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider / Number images used: 11329 |
Final angle assignment | Details: SPIDER:theta 90 degrees, phi 60 degrees |
-Atomic model buiding 1
Initial model | (PDB ID: , ) |
---|---|
Software | Name: colores |
Details | Protocol: rigid body. The receptor-binding domain (1TYX) of the tailspike was computationally docked with the program colores, and the docking was unambiguous. Then the head-binding domain (1LKT) was manually docked. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient |