+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5012 | |||||||||
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Title | Bacteriophage lambda stabilization by auxiliary protein gpD | |||||||||
Map data | mature wild type phage lambda | |||||||||
Sample |
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Keywords | bacteriophage / phage / lambda / icosahedral / capsid / cryoEM | |||||||||
Biological species | Enterobacteria phage (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.8 Å | |||||||||
Authors | Lander GC / Evilevitch A / Jeembaeva M / Potter CS / Carragher B / Johnson JE | |||||||||
Citation | Journal: Structure / Year: 2008 Title: Bacteriophage lambda stabilization by auxiliary protein gpD: timing, location, and mechanism of attachment determined by cryo-EM. Authors: Gabriel C Lander / Alex Evilevitch / Meerim Jeembaeva / Clinton S Potter / Bridget Carragher / John E Johnson / Abstract: We report the cryo-EM structure of bacteriophage lambda and the mechanism for stabilizing the 20-A-thick capsid containing the dsDNA genome. The crystal structure of the HK97 bacteriophage capsid ...We report the cryo-EM structure of bacteriophage lambda and the mechanism for stabilizing the 20-A-thick capsid containing the dsDNA genome. The crystal structure of the HK97 bacteriophage capsid fits most of the T = 7 lambda particle density with only minor adjustment. A prominent surface feature at the 3-fold axes corresponds to the cementing protein gpD, which is necessary for stabilization of the capsid shell. Its position coincides with the location of the covalent cross-link formed in the docked HK97 crystal structure, suggesting an evolutionary replacement of this gene product in lambda by autocatalytic chemistry in HK97. The crystal structure of the trimeric gpD, in which the 14 N-terminal residues required for capsid binding are disordered, fits precisely into the corresponding EM density. The N-terminal residues of gpD are well ordered in the cryo-EM density, adding a strand to a beta-sheet formed by the capsid proteins and explaining the mechanism of particle stabilization. | |||||||||
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_5012.map.gz | 84.7 MB | EMDB map data format | |
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Header (meta data) | emd-5012-v30.xml emd-5012.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | emd_5012_1.tif | 687.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5012 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5012 | HTTPS FTP |
-Validation report
Summary document | emd_5012_validation.pdf.gz | 78.4 KB | Display | EMDB validaton report |
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Full document | emd_5012_full_validation.pdf.gz | 77.5 KB | Display | |
Data in XML | emd_5012_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5012 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5012 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5012.map.gz / Format: CCP4 / Size: 105.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | mature wild type phage lambda | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.02 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 : Mature wild type bacteriophage lambda
Entire | Name: Mature wild type bacteriophage lambda |
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Components |
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-Supramolecule #1000: Mature wild type bacteriophage lambda
Supramolecule | Name: Mature wild type bacteriophage lambda / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1 |
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Molecular weight | Experimental: 20.9 MDa / Theoretical: 20.9 MDa |
-Supramolecule #1: Enterobacteria phage
Supramolecule | Name: Enterobacteria phage / type: virus / ID: 1 / Name.synonym: Bacteriophage lambda / Sci species name: Enterobacteria phage / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Bacteriophage lambda |
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Host (natural) | Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA) |
Virus shell | Shell ID: 1 / Name: gpE / Diameter: 650 Å / T number (triangulation number): 7 |
-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: 7.4 / Details: 10mM MgSO4, 50mM Tris-HCl |
Grid | Details: 400 mesh copper grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot / Method: double-blotted for 7 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Min: 78 K / Max: 78 K / Average: 78 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmation corrected at 135,000 times magnification |
Date | Sep 23, 2007 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Number real images: 8058 / Average electron dose: 19 e/Å2 / Camera length: 61.4 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder: Side entry cryostage / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Details | Protocol: rigid body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |