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Icosahedral reconstruction of bacteriophage P2 procapsid
by single particle (icosahedral) reconstruction, at 8.0 A resolution
#1: Surface view with section colored by density value, Surface level: 2, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 2, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5406 |
|---|---|
| Title | Icosahedral reconstruction of bacteriophage P2 procapsid |
| Map | Reconstruction of bacteriophage P2 procapsid |
| Sample | Bacteriophage P2 procapsid |
| Keywords |  bacteriophage, P2, P4, capsid, procapsid, assembly, size determination, scaffolding protein, triangulation numbers, T=7 dextro, Sid, gpN |
| Authors | Dearborn AD, Laurinmaki P, Chandramouli P, Rodenburg CM, Wang S, Butcher SJ, Dokland T |
| Date | Deposition: 2012-02-20, Header release: 2012-02-22, Map release: 2012-05-29, Last update: 2012-05-29 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 2, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 2, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | J. Struct. Biol., Vol. 178, Issue 3, Page 215-24, Year 2012 |
|---|---|
| Title | Structure and size determination of bacteriophage P2 and P4 procapsids: function of size responsiveness mutations. |
| Authors | Altaira D Dearborn, Pasi Laurinmaki, Preethi Chandramouli, Cynthia M Rodenburg, Sifang Wang, Sarah J Butcher, Terje Dokland Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA. |
| Keywords | Bacteriophage P2 (chemistry), Capsid (chemistry), Cryoelectron Microscopy, Models, Biological, Mutation, Myoviridae (chemistry), Protein Structure, Secondary |
| Links | PII: S1047-8477(12)00105-0, DOI: 10.1016/j.jsb.2012.04.002, PubMed: 22508104, PMC: PMC3361666 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5406.map ( map file in CCP4 format, 131074 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A = 655.36005 A , B = 655.36005 A , C = 655.36005 A , alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 2.048 A , Y = 2.048 A , Z = 2.048 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Reconstruction of bacteriophage P2 procapsid | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | Bacteriophage P2 procapsid |
|---|---|
| Number of Components | 2 |
| Oligomeric State | 420 copies of gpN and 100-150 copies of gpO |
| Theoretical Mass | 16.884 MDa |
| Details | gpO is disordered and not visible in the map |
| Component #1: protein - N*, major capsid protein | |
| Scientific name | gpN |
| Common Name | N*, major capsid protein |
| Theoretical Mass | 16.884 MDa |
| Oligomeric Details | icosahedral |
| Scientific Name of Species | Escherichia coli (NCBI Taxonomy: 562)
|
| Common Name of Species | Escherichia coli |
| Strain | BL21(DE3) |
| Recombinant expression | Yes |
| Engineered Source | Vector: pET21 Exp System: Escherichia coli (NCBI Taxonomy: 562) |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 1.0 mg/ml |
|---|---|
| Specimen Support Details | 200 mesh Quantifoil R2/2 or Lacey carbon |
| Specimen State | particle |
| Buffer | Details: 10 mM Tris-HCl, pH 8.0, 20 mM NaCl, 1 mM MgCl2 pH: 8.0 |
| Vitrification | |
| Method | Blot for 2 sec before plunging |
| Cryogen Name | ETHANE |
| Instrument | HOMEMADE PLUNGER |
| Temperature | 110 Kelvin |
| Imaging | |
| Microscope | FEI TECNAI F20 |
| Date | 22-APR-2011 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 20 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 50000 X, Calibrated: 50000 X |
| Nominal Cs | 2.0 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 900 nm - 3000 nm |
| Specimen Holder | |
| Holder | ( GATAN LIQUID NITROGEN ) |
| Temperature | 97 Kelvin ( 95 Kelvin - 99 Kelvin ) |
| Camera | |
| Detector | Kodak SO-163 film |
| Image Acquisition | |
| Scanner | NIKON SUPER COOLSCAN 9000 |
| Sampling Size | 12.7 microns |
| Quant Bit Number | 16 |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | projection matching, polar Fourier transform |
| Software | EMAN,AUTO3DEM |
| CTF Correction | Each micrograph |
| Resolution By Author | 8.0 |
| Resolution Method | FSC at 0.25 cutoff |
| Single Particle | |
| Number of Projections | 7582 |
| Applied Symmetry | I (icosahedral) |
| Atomic Model Fitting | |
| Model #0 | |
| Details | Protocol: Rigid body fitting of individual subsegments |
| Software | Chimera |
| Refinement Protocol | rigid body |
| Refinement Space | REAL |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-5406.xml (7.8 KB) | ||
|---|---|---|---|
| Map data | emd_5406.map.gz (117.2 MB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5406 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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