+
Open data
-
Basic information
| Entry | Database: PDB / ID: 9mog | |||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Title | Structure of the distal part of the bacteriophage T4 tail | |||||||||||||||||||||||||||
Components |
| |||||||||||||||||||||||||||
Keywords | VIRAL PROTEIN / bacteriophage T4 / contractile tail / baseplate | |||||||||||||||||||||||||||
| Function / homology | Function and homology informationvirus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / viral release from host cell / peptidoglycan catabolic process / virion component ...virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / viral release from host cell / peptidoglycan catabolic process / virion component / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / entry receptor-mediated virion attachment to host cell / defense response to bacterium / symbiont entry into host cell / structural molecule activity / metal ion binding / identical protein binding Similarity search - Function | |||||||||||||||||||||||||||
| Biological species | Escherichia phage T4 (virus) | |||||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||||||||||||||
Authors | Fokine, A. / Zhu, J. / Klose, T. / Vago, F. / Arnaud, C. / Wang, Z. / Khare, B. / Rossmann, M.G. / Chen, Z. / Sun, L. ...Fokine, A. / Zhu, J. / Klose, T. / Vago, F. / Arnaud, C. / Wang, Z. / Khare, B. / Rossmann, M.G. / Chen, Z. / Sun, L. / Fang, Q. / Kuhn, R. / Rao, V.B. | |||||||||||||||||||||||||||
| Funding support | United States, 1items
| |||||||||||||||||||||||||||
Citation | Journal: To Be PublishedTitle: In situ Atomic Structure of Phage T4 Head-Tail Connector Complex Shows Molecular Gates Open for Genome Ejection and DNA Pushed into the Tail Tube Authors: Fokine, A. / Zhu, J. / Klose, T. / Vago, F. / Arnaud, C. / Wang, Z. / Khare, B. / Rossmann, M.G. / Chen, Z. / Sun, L. / Fang, Q. / Kuhn, R. / Rao, V.B. | |||||||||||||||||||||||||||
| History |
|
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 9mog.cif.gz | 13.4 MB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb9mog.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 9mog.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/9mog ftp://data.pdbj.org/pub/pdb/validation_reports/mo/9mog | HTTPS FTP |
|---|
-Related structure data
| Related structure data | ![]() 48459MC ![]() 9mkbC ![]() 9mofC ![]() 9mohC M: map data used to model this data C: citing same article ( |
|---|---|
| Similar structure data | Similarity search - Function & homology F&H Search |
-
Links
-
Assembly
| Deposited unit | ![]()
|
|---|---|
| 1 |
|
-
Components
-Protein , 17 types, 202 molecules S0S1S2S3S4S5S6S7S8SASOSPSQSvSwSxSySzT1T2T3T4T5T6T7T8T9TFTGTH...
| #1: Protein | Mass: 56253.926 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P10930#2: Protein | Mass: 31024.725 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SWG4#3: Protein | Mass: 23725.523 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SW18#4: Protein | Mass: 66281.680 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P10928#5: Protein | Mass: 119336.516 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P19061#6: Protein | Mass: 38041.668 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SVZ9#7: Protein | Mass: 71348.625 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SVW9#8: Protein | Mass: 74492.641 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P19060#9: Protein | Mass: 63183.723 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SVH6, lysozyme#10: Protein | | Mass: 10233.663 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SVS3#11: Protein | Mass: 18479.613 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SVI2#12: Protein | Mass: 44431.062 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9XHP4#13: Protein | Mass: 64485.539 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P13337#14: Protein | Mass: 22990.885 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9XI21#15: Protein | Mass: 15111.101 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SW44#16: Protein | Mass: 39770.332 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SVT9#17: Protein | Mass: 35001.188 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P13341 |
|---|
-Unassigned peptide ... , 5 types, 18 molecules rcrdrerfrgrhsQsTsUtStXtYuRuVuWvZvavb
| #18: Protein/peptide | Mass: 2145.636 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus)#19: Protein/peptide | Mass: 1549.902 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus)#20: Protein/peptide | Mass: 869.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus)#21: Protein/peptide | Mass: 613.749 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus)#22: Protein/peptide | Mass: 783.958 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) |
|---|
-Non-polymers , 1 types, 6 molecules 
| #23: Chemical | ChemComp-ZN / |
|---|
-Details
| Has ligand of interest | N |
|---|---|
| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
|---|---|
| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
| Component | Name: Escherichia phage T4 / Type: VIRUS / Entity ID: #1-#9 / Source: NATURAL |
|---|---|
| Source (natural) | Organism: Escherichia phage T4 (virus) |
| Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
| Natural host | Organism: Escherichia coli / Strain: B |
| Buffer solution | pH: 7.5 |
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
| Specimen support | Grid type: PELCO Ultrathin Carbon with Lacey Carbon |
| Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: Ted Pella lacey carbon 400 mesh grids (catalog No: 01824) were used. |
-
Electron microscopy imaging
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
|---|---|
| Microscopy | Model: TFS KRIOS |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm |
| Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
| Image recording | Electron dose: 38 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-
Processing
| EM software | Name: PHENIX / Version: 1.21.1_5286 / Category: model refinement |
|---|---|
| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
| Symmetry | Point symmetry: C3 (3 fold cyclic) |
| 3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113800 / Symmetry type: POINT |
Movie
Controller
About Yorodumi




Escherichia phage T4 (virus)
United States, 1items
Citation









PDBj






FIELD EMISSION GUN