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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5150 | |||||||||
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Title | P22 Heat Expanded Head | |||||||||
![]() | This is a density map of heat expanded bacteriophage P22 particles | |||||||||
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Function / homology | Major capsid protein Gp5 / P22 coat protein - gene protein 5 / viral procapsid / viral procapsid maturation / T=7 icosahedral viral capsid / viral capsid / identical protein binding / Major capsid protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.2 Å | |||||||||
![]() | Parent KN / Khayat R / Tu LH / Suhanovsky MM / Cortines JR / Teschke CM / Johnson JE / Baker TS | |||||||||
![]() | ![]() Title: P22 coat protein structures reveal a novel mechanism for capsid maturation: stability without auxiliary proteins or chemical crosslinks. Authors: Kristin N Parent / Reza Khayat / Long H Tu / Margaret M Suhanovsky / Juliana R Cortines / Carolyn M Teschke / John E Johnson / Timothy S Baker / ![]() Abstract: Viral capsid assembly and stability in tailed, dsDNA phage and Herpesviridae are achieved by various means including chemical crosslinks (unique to HK97), or auxiliary proteins (lambda, T4, phi29, ...Viral capsid assembly and stability in tailed, dsDNA phage and Herpesviridae are achieved by various means including chemical crosslinks (unique to HK97), or auxiliary proteins (lambda, T4, phi29, and herpesviruses). All these viruses have coat proteins (CP) with a conserved, HK97-like core structure. We used a combination of trypsin digestion, gold labeling, cryo-electron microscopy, 3D image reconstruction, and comparative modeling to derive two independent, pseudoatomic models of bacteriophage P22 CP: before and after maturation. P22 capsid stabilization results from intersubunit interactions among N-terminal helices and an extensive "P loop," which obviate the need for crosslinks or auxiliary proteins. P22 CP also has a telokin-like Ig domain that likely stabilizes the monomer fold so that assembly may proceed via individual subunit addition rather than via preformed capsomers as occurs in HK97. Hence, the P22 CP structure may be a paradigm for understanding how monomers assemble in viruses like phi29 and HSV-1. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 107.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.3 KB 10.3 KB | Display Display | ![]() |
Images | ![]() | 756.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3iyhMC ![]() 5149C ![]() 3iyiC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | This is a density map of heat expanded bacteriophage P22 particles | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : P22 Heat Expanded Heads
Entire | Name: P22 Heat Expanded Heads |
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Components |
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-Supramolecule #1000: P22 Heat Expanded Heads
Supramolecule | Name: P22 Heat Expanded Heads / type: sample / ID: 1000 / Oligomeric state: Icosahedral / Number unique components: 1 |
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-Supramolecule #1: Enterobacteria phage P22
Supramolecule | Name: Enterobacteria phage P22 / type: virus / ID: 1 / Name.synonym: Phage P22 / NCBI-ID: 10754 / Sci species name: Enterobacteria phage P22 / Database: NCBI / Virus type: OTHER / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: Phage P22 |
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Host (natural) | Organism: ![]() synonym: BACTERIA(EUBACTERIA) |
Virus shell | Shell ID: 1 / Diameter: 680 Å / T number (triangulation number): 7 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 7.6 / Details: 20 mM sodium phosphate |
Grid | Details: Quantifoil grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 89 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunge-freezer / Method: blot 2-3 seconds before plunging |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 90 K / Max: 90 K / Average: 90 K |
Alignment procedure | Legacy - Astigmatism: at working magnification |
Date | Aug 10, 2009 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 58 / Average electron dose: 8 e/Å2 / Bits/pixel: 16 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 3.16 µm / Nominal defocus min: 0.63 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder: Polara Multi Specimen Holder / Specimen holder model: OTHER |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
Details | data were collected on film |
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CTF correction | Details: ROBEM |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Details: Final map was calculated at 7.0A resolution / Number images used: 3308 |