+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1507 | |||||||||
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Title | cryoEM structure of bacteriophage lambda procapsid | |||||||||
Map data | lambda prohead reconstruction | |||||||||
Sample |
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Keywords | bacteriophage / phage / procapsid / prophage / lambda / icosahedral / cryoEM | |||||||||
Biological species | Enterobacteria phage lambda (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.5 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_1507.map.gz | 19.1 MB | EMDB map data format | |
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Header (meta data) | emd-1507-v30.xml emd-1507.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | 1507.gif | 77.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1507 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1507 | HTTPS FTP |
-Validation report
Summary document | emd_1507_validation.pdf.gz | 215.1 KB | Display | EMDB validaton report |
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Full document | emd_1507_full_validation.pdf.gz | 214.3 KB | Display | |
Data in XML | emd_1507_validation.xml.gz | 4.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1507 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1507 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1507.map.gz / Format: CCP4 / Size: 105.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | lambda prohead reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.26 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 : lambda procapsid
Entire | Name: lambda procapsid |
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Components |
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-Supramolecule #1000: lambda procapsid
Supramolecule | Name: lambda procapsid / type: sample / ID: 1000 Details: particles were present in a preparation of a 37.7 kbp packaging lambda mutant Oligomeric state: icosahedral / Number unique components: 1 |
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Molecular weight | Experimental: 16 MDa / Theoretical: 16 MDa |
-Supramolecule #1: Enterobacteria phage lambda
Supramolecule | Name: Enterobacteria phage lambda / type: virus / ID: 1 / Name.synonym: capsid, gpE / NCBI-ID: 10710 / Sci species name: Enterobacteria phage lambda / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: capsid, gpE |
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Host (natural) | Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA) |
Molecular weight | Experimental: 16 MDa / Theoretical: 16 MDa |
Virus shell | Shell ID: 1 / Name: gpE / Diameter: 500 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 | 0.5 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 blot for 7 seconds |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Min: 77 K / Max: 78 K / Average: 78 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 135,000 times magnification |
Date | Feb 16, 2007 |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Number real images: 2683 / Average electron dose: 19 e/Å2 / Camera length: 61.4 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50000 / 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: 50000 |
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: UCSF Chimera |
Details | Protocol: rigid body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |