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- EMDB-5690: Cryo-electron microscopy of T7 tail complex formed by gp8, gp11, ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5690 | |||||||||
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Title | Cryo-electron microscopy of T7 tail complex formed by gp8, gp11, and gp12 proteins | |||||||||
![]() | Reconstuction of T7 tail complex formed by proteins gp8, gp11, and gp12 | |||||||||
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![]() | Bacteriophage / DNA ejection / tail complex / connector / gatekeeper | |||||||||
Function / homology | ![]() virus tail, tube / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.0 Å | |||||||||
![]() | Cuervo A / Pulido-Cid M / Chagoyen M / Arranz R / Gonzalez-Garcia VA / Garcia-Doval C / Caston JR / Valpuesta JM / van Raaij MJ / Martin-Benito J / Carrascosa JL | |||||||||
![]() | ![]() Title: Structural characterization of the bacteriophage T7 tail machinery. Authors: Ana Cuervo / Mar Pulido-Cid / Mónica Chagoyen / Rocío Arranz / Verónica A González-García / Carmela Garcia-Doval / José R Castón / José M Valpuesta / Mark J van Raaij / Jaime Martín- ...Authors: Ana Cuervo / Mar Pulido-Cid / Mónica Chagoyen / Rocío Arranz / Verónica A González-García / Carmela Garcia-Doval / José R Castón / José M Valpuesta / Mark J van Raaij / Jaime Martín-Benito / José L Carrascosa / ![]() Abstract: Most bacterial viruses need a specialized machinery, called "tail," to inject their genomes inside the bacterial cytoplasm without disrupting the cellular integrity. Bacteriophage T7 is a well ...Most bacterial viruses need a specialized machinery, called "tail," to inject their genomes inside the bacterial cytoplasm without disrupting the cellular integrity. Bacteriophage T7 is a well characterized member of the Podoviridae family infecting Escherichia coli, and it has a short noncontractile tail that assembles sequentially on the viral head after DNA packaging. The T7 tail is a complex of around 2.7 MDa composed of at least four proteins as follows: the connector (gene product 8, gp8), the tail tubular proteins gp11 and gp12, and the fibers (gp17). Using cryo-electron microscopy and single particle image reconstruction techniques, we have determined the precise topology of the tail proteins by comparing the structure of the T7 tail extracted from viruses and a complex formed by recombinant gp8, gp11, and gp12 proteins. Furthermore, the order of assembly of the structural components within the complex was deduced from interaction assays with cloned and purified tail proteins. The existence of common folds among similar tail proteins allowed us to obtain pseudo-atomic threaded models of gp8 (connector) and gp11 (gatekeeper) proteins, which were docked into the corresponding cryo-EM volumes of the tail complex. This pseudo-atomic model of the connector-gatekeeper interaction revealed the existence of a common molecular architecture among viruses belonging to the three tailed bacteriophage families, strongly suggesting that a common molecular mechanism has been favored during evolution to coordinate the transition between DNA packaging and tail assembly. | |||||||||
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 | ![]() | 1.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.6 KB 13.6 KB | Display Display | ![]() |
Images | ![]() | 94.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3j4aMC ![]() 3j4bMC ![]() 5689C ![]() 5713C 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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Map
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Annotation | Reconstuction of T7 tail complex formed by proteins gp8, gp11, and gp12 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.75 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 : T7 tail complex formed by proteins gp8, gp11, and gp12
Entire | Name: T7 tail complex formed by proteins gp8, gp11, and gp12 |
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Components |
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-Supramolecule #1000: T7 tail complex formed by proteins gp8, gp11, and gp12
Supramolecule | Name: T7 tail complex formed by proteins gp8, gp11, and gp12 type: sample / ID: 1000 / Oligomeric state: gp8 (12mer), gp11 (12mer), gp12 (6mer) / Number unique components: 3 |
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Molecular weight | Theoretical: 1.5 MDa |
-Macromolecule #1: gp8
Macromolecule | Name: gp8 / type: protein_or_peptide / ID: 1 / Name.synonym: Connector / Number of copies: 12 / Oligomeric state: 12mer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 59 KDa |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #2: gp11
Macromolecule | Name: gp11 / type: protein_or_peptide / ID: 2 / Name.synonym: gatekeeper / Details: This protein was cloned with and His-tag / Number of copies: 12 / Oligomeric state: 12mer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 25 KDa |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #3: gp12
Macromolecule | Name: gp12 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Oligomeric state: 6mer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 90 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.8 / Details: 50mM Tris-HCl, 10mM MgCl2, 100 mM NaCl |
Grid | Details: R2/2 Quantifoil coated with a thin carbon layer |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM CPC Method: Samples were applied to grids for 1 minute, blotted, and plunged into liquid ethane. |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Min: 91 K / Max: 113 K |
Date | Nov 8, 2012 |
Image recording | Category: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Number real images: 264 / Average electron dose: 10 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 108696 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 108696 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: each micrograph |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: XMIPP, SPIDER, EMAN / Number images used: 1820 |
-Atomic model buiding 1
Initial model | PDB ID: ![]() 1vt0 |
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Software | Name: ![]() |
Details | One monomer was manually fitted and then the oligomer was generated using SITUS program. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Volumetric correlation |
Output model | ![]() PDB-3j4a: ![]() PDB-3j4b: |
-Atomic model buiding 2
Initial model | PDB ID: Chain - Chain ID: L |
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Software | Name: ![]() |
Details | One monomer was manually fitted and then the oligomer was generated using SITUS program. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Volumetric correlation |
Output model | ![]() PDB-3j4a: ![]() PDB-3j4b: |