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- EMDB-1572: The T4 packaging motor, T4 procapsid with large terminase gp17 bound -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1572 | |||||||||
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Title | The T4 packaging motor, T4 procapsid with large terminase gp17 bound | |||||||||
![]() | The T4 packaging motor, T4 procapsid with large terminase gp17 bound. | |||||||||
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![]() | procapsid / DNA packaging motor / large terminase | |||||||||
Function / homology | ![]() viral terminase, large subunit / DNA nuclease activity / viral genome packaging / viral procapsid maturation / viral DNA genome packaging / nuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / chromosome organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity ...viral terminase, large subunit / DNA nuclease activity / viral genome packaging / viral procapsid maturation / viral DNA genome packaging / nuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / chromosome organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity / ATP hydrolysis activity / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 34.0 Å | |||||||||
![]() | Sun S / Kondabagil K / Draper B / Alam TI / Bowman VD / Zhang Z / Hegde S / Fokine A / Rossmann MG / Rao VB | |||||||||
![]() | ![]() Title: The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces. Authors: Siyang Sun / Kiran Kondabagil / Bonnie Draper / Tanfis I Alam / Valorie D Bowman / Zhihong Zhang / Shylaja Hegde / Andrei Fokine / Michael G Rossmann / Venigalla B Rao / ![]() Abstract: Viral genomes are packaged into "procapsids" by powerful molecular motors. We report the crystal structure of the DNA packaging motor protein, gene product 17 (gp17), in bacteriophage T4. The ...Viral genomes are packaged into "procapsids" by powerful molecular motors. We report the crystal structure of the DNA packaging motor protein, gene product 17 (gp17), in bacteriophage T4. The structure consists of an N-terminal ATPase domain, which provides energy for compacting DNA, and a C-terminal nuclease domain, which terminates packaging. We show that another function of the C-terminal domain is to translocate the genome into the procapsid. The two domains are in close contact in the crystal structure, representing a "tensed state." A cryo-electron microscopy reconstruction of the T4 procapsid complexed with gp17 shows that the packaging motor is a pentamer and that the domains within each monomer are spatially separated, representing a "relaxed state." These structures suggest a mechanism, supported by mutational and other data, in which electrostatic forces drive the DNA packaging by alternating between tensed and relaxed states. Similar mechanisms may occur in other molecular motors. | |||||||||
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 | ![]() | 21 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.7 KB 9.7 KB | Display Display | ![]() |
Images | ![]() | 131.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 358.3 KB | Display | ![]() |
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Full document | ![]() | 357.9 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ezkMC ![]() 1573C ![]() 3c6aC ![]() 3c6hC ![]() 3cpeC 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The T4 packaging motor, T4 procapsid with large terminase gp17 bound. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.48 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 : T4 procapsid with gp17 bound
Entire | Name: T4 procapsid with gp17 bound |
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Components |
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-Supramolecule #1000: T4 procapsid with gp17 bound
Supramolecule | Name: T4 procapsid with gp17 bound / type: sample / ID: 1000 / Number unique components: 2 |
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-Supramolecule #1: Enterobacteria phage T4
Supramolecule | Name: Enterobacteria phage T4 / type: virus / ID: 1 / Name.synonym: bacteriophage T4 / NCBI-ID: 10665 / Sci species name: Enterobacteria phage T4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: bacteriophage T4 |
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Host (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 Details: 50mM Tris-HCl, 100mM NaCl, 5mM MgCl2, 3mM beta-mercaptoethanol |
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Grid | Details: quantifoil copper grid 2um holes |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: in-house, gravity driven plunger Method: 3.5ul of sample hand blotted approx. 1sec |
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Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Temperature | Average: 97 K |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.25 µm / Number real images: 108 / Average electron dose: 20 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 39190 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 38000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
CTF correction | Details: phase flipping for each micrograph |
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Final reconstruction | Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider / Number images used: 1716 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: EMFIT |
Details | Protocol: Rigid Body. The N- and C-terminal domains of gp17 were separately fitted into their corresponding cryoEM densities |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-3ezk: |