+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5049 | |||||||||
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Title | 12-fold assembly-naive P22 portal | |||||||||
Map data | 12-fold P22 portal | |||||||||
Sample |
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Keywords | p22 bacteriophage phage portal virus connector | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.6 Å | |||||||||
Authors | Lander GC / Khayat R / Li R / Prevelige PE / Potter CS / Carragher B / Johnson JE | |||||||||
Citation | Journal: Structure / Year: 2009 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 |
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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_5049.map.gz | 10.5 MB | EMDB map data format | |
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Header (meta data) | emd-5049-v30.xml emd-5049.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | emd_5049_1.tif | 274.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5049 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5049 | HTTPS FTP |
-Validation report
Summary document | emd_5049_validation.pdf.gz | 78.4 KB | Display | EMDB validaton report |
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Full document | emd_5049_full_validation.pdf.gz | 77.5 KB | Display | |
Data in XML | emd_5049_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5049 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5049 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5049.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 12-fold P22 portal | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.95 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 : P22 gp1 subunit
Entire | Name: P22 gp1 subunit |
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Components |
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-Supramolecule #1000: P22 gp1 subunit
Supramolecule | Name: P22 gp1 subunit / type: sample / ID: 1000 Oligomeric state: heterogenous mixture of 11- and 12-fold rings Number unique components: 1 |
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Molecular weight | Experimental: 992 KDa / Theoretical: 992 KDa |
-Macromolecule #1: gp1
Macromolecule | Name: gp1 / type: protein_or_peptide / ID: 1 / Name.synonym: portal / Number of copies: 12 / Oligomeric state: 11-mers and 12-mers / Recombinant expression: No / Database: NCBI |
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Source (natural) | Cell: E. coli strain BL21 |
Molecular weight | Experimental: 82.7 KDa / Theoretical: 82.7 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.5 Details: 20mM Hepes, pH 7.5, 50 mM sodium chloride, 5mM beta-mercaptoethanol |
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 |
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Temperature | Average: 4.5 K |
Alignment procedure | Legacy - Astigmatism: corrected at 210,000 times mag |
Date | May 13, 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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.4 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 80000 |
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. |
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CTF correction | Details: each particle with EMAN |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, SPIDER / Number images used: 23660 |
Final two d classification | Number classes: 1000 |