+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-5051 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | P22 tail machine | |||||||||
![]() | P22 tail machine | |||||||||
![]() |
| |||||||||
![]() | p22 bacteriophage phage tail machine tail spikes infection | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.4 Å | |||||||||
![]() | Lander GC / Khayat R / Li R / Prevelige PE / Potter CS / Carragher B / Johnson JE | |||||||||
![]() | ![]() Title: The P22 tail machine at subnanometer resolution reveals the architecture of an infection conduit. Authors: Gabriel C Lander / Reza Khayat / Rui Li / Peter E Prevelige / Clinton S Potter / Bridget Carragher / John E Johnson / ![]() Abstract: The portal channel is a key component in the life cycle of bacteriophages and herpesviruses. The bacteriophage P22 portal is a 1 megadalton dodecameric oligomer of gp1 that plays key roles in capsid ...The portal channel is a key component in the life cycle of bacteriophages and herpesviruses. The bacteriophage P22 portal is a 1 megadalton dodecameric oligomer of gp1 that plays key roles in capsid assembly, DNA packaging, assembly of the infection machinery, and DNA ejection. The portal is the nucleation site for the assembly of 39 additional subunits generated from multiple copies of four gene products (gp4, gp10, gp9, and gp26), which together form the multifunctional tail machine. These components are organized with a combination of 12-fold (gp1, gp4), 6-fold (gp10, trimers of gp9), and 3-fold (gp26, gp9) symmetry. Here we present the 3-dimensional structures of the P22 assembly-naive portal formed from expressed subunits (gp1) and the intact tail machine purified from infectious virions. The assembly-naive portal structure exhibits a striking structural similarity to the structures of the portal proteins of SPP1 and phi29 derived from X-ray crystallography. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 10.7 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 10.7 KB 10.7 KB | Display Display | ![]() |
Images | ![]() | 184.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 77.3 KB | Display | |
Data in XML | ![]() | 491 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | P22 tail machine | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : P22 tail machine
Entire | Name: P22 tail machine |
---|---|
Components |
|
-Supramolecule #1000: P22 tail machine
Supramolecule | Name: P22 tail machine / type: sample / ID: 1000 Oligomeric state: 12 gp1, 12 gp4, 6 gp10, 6 trimers of gp9, trimer of gp26 Number unique components: 5 |
---|---|
Molecular weight | Experimental: 2.891 MDa / Theoretical: 2.891 MDa |
-Macromolecule #1: tail machine
Macromolecule | Name: tail machine / type: protein_or_peptide / ID: 1 / Name.synonym: tail machine / Recombinant expression: Yes |
---|---|
Source (natural) | Cell: salmonella enterica |
Molecular weight | Experimental: 2.8917 MDa / Theoretical: 2.8917 MDa |
Recombinant expression | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 4 mg/mL |
---|---|
Buffer | pH: 8 / Details: 50mM Na2HPO4, pH 8.0 |
Grid | Details: C-flats from Protochips |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4.5 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: blot for 6 seconds, offset -2 |
-
Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Temperature | Average: 4.5 K |
Alignment procedure | Legacy - Astigmatism: corrected at 210,000 times mag |
Date | Feb 14, 2008 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: gatan ct3500 / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
-
Image processing
Details | particles selected using a difference of gaussians particle picker. |
---|---|
CTF correction | Details: each particle with EMAN |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, SPIDER / Number images used: 358893 |
Final two d classification | Number classes: 1000 |
-Atomic model buiding 1
Initial model | PDB ID: |
---|---|
Software | Name: ![]() |
Details | Protocol: rigid body. Manual fit using chimera, then used Fit in Map function |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 2
Initial model | PDB ID: |
---|---|
Software | Name: ![]() |
Details | Protocol: rigid body. Manual fit using chimera, then used Fit in Map function |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |