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Domain-wise fitting of the crystal structure of T.thermophilus EF-G into the low resolution map of the release complex.Puromycin.EFG.GDPNP of E.coli 70S ribosome.
by single particle reconstruction, at 10.8 A resolution
#1: Depositted structure unit, Made by Jmol
#2: Superimposing with simplified surface model of EM map, EMDB-1055, Made by Jmol
#3: Superimposing with simplified surface model of EM map, EMDB-1362, Made by Jmol
#4: Superimposing with simplified surface model of EM map, EMDB-1363, Made by Jmol
#5: Superimposing with simplified surface model of EM map, EMDB-1365, Made by Jmol
#6: Superimposing with simplified surface model of EM map, EMDB-1366, Made by Jmol
#7: With PDB-1pn7, PDB-1pn8, Made by Jmol
#8: Superimposing with EM 3D map: EMDB-1055 (with PDB-1pn7, PDB-1pn8), Made by UCSF CHIMERA
#9: Superimposing with EM 3D map: EMDB-1362, Made by UCSF CHIMERA
#10: Superimposing with EM 3D map: EMDB-1363 (with PDB-1pn7, PDB-1pn8), Made by UCSF CHIMERA
#11: Superimposing with EM 3D map: EMDB-1364, Made by UCSF CHIMERA
#12: Superimposing with EM 3D map: EMDB-1365 (with PDB-1pn7, PDB-1pn8), Made by UCSF CHIMERA
#13: Superimposing with EM 3D map: EMDB-1366, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 1pn6 |
|---|---|
| Title | Domain-wise fitting of the crystal structure of T.thermophilus EF-G into the low resolution map of the release complex.Puromycin.EFG.GDPNP of E.coli 70S ribosome. |
| Descriptor | Elongation factor G |
| Keywords |  BIOSYNTHETIC PROTEIN, Elongation Factor-G, E.coli 70S ribosome, Post-termination complex, Fitting of crystal structure, Cryo-EM |
| PDBj Mine pages |  Summary, Structural Details, Experimental Details, Functional Details |
| Other databases | RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST |
| Structure Visualization | |
| Movies |  Movie Page#1: Depositted structure unit, Made by Jmol #2: Superimposing with simplified surface model of EM map, EMDB-1055, Made by Jmol #3: Superimposing with simplified surface model of EM map, EMDB-1362, Made by Jmol #4: Superimposing with simplified surface model of EM map, EMDB-1363, Made by Jmol #5: Superimposing with simplified surface model of EM map, EMDB-1365, Made by Jmol #6: Superimposing with simplified surface model of EM map, EMDB-1366, Made by Jmol #7: With PDB-1pn7, PDB-1pn8, Made by Jmol #8: Superimposing with EM 3D map: EMDB-1055 (with PDB-1pn7, PDB-1pn8), Made by UCSF CHIMERA #9: Superimposing with EM 3D map: EMDB-1362, Made by UCSF CHIMERA #10: Superimposing with EM 3D map: EMDB-1363 (with PDB-1pn7, PDB-1pn8), Made by UCSF CHIMERA #11: Superimposing with EM 3D map: EMDB-1364, Made by UCSF CHIMERA #12: Superimposing with EM 3D map: EMDB-1365 (with PDB-1pn7, PDB-1pn8), Made by UCSF CHIMERA #13: Superimposing with EM 3D map: EMDB-1366, Made by UCSF CHIMERA |
| Structure viewers |  Yorodumi, jV4, Jmol,  Biological unit (Images, jV) |
| Related Structure Data | |
| Related Entries |
Fit: target map of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - primary | |
| Article | Cell(Cambridge,Mass.), Vol. 114, Page: 123 - 134, Year: 2003, |
|---|---|
| Title | Locking and Unlocking of Ribosomal Motions |
| Authors | Valle, M., Zavialov, A., Sengupta, J., Rawat, U., Ehrenberg, M., Frank, J. |
| Links | DOI: 10.1016/S0092-8674(03)00476-8 |
| Citation - 1 | |
| Article | J.Mol.Biol., Vol. 303, Page: 593 - 603, Year: 2000, |
| Title | STRUCTURE OF A MUTANT EF-G REVEALS DOMAIN III AND POSSIBLY THE FUSIDIC ACID BINDING SITE |
| Citation - 2 | |
| Article | Proc.Natl.Acad.Sci.USA, Vol. 95, Page: 6134 - 6138, Year: 1998, |
| Title | Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation. |
| Citation - 3 | |
| Article | Cell(Cambridge,Mass.), Vol. 107, Page: 1 - 20, Year: 2001, |
| Title | A posttermination ribosomal complex is the guanine exchange factor for peptide reslease factor RF3. |
 Components | |
| ID 1 : EF-G | |
| Image |   |
|---|---|
| Description | Elongation factor G |
| Type | polypeptide(L) |
| Formula weight | 76910.844 Da |
| Number of molecules | 1 |
| ID | 1 |
| Source | Method: Isolated from a natural source Genus: Thermus NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: P13551, Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Entity assembly | |
| Assembly-ID | 1 |
| GO-ID | GO:0006414 |
| InterPro-ID | IPR:004540 |
| Name | ELONGATION FACTOR G |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| pH | 7.5 |
| Sample concentration | 32 mg/ml |
| Sample support | |
| Details | Quantifoil holley-carbon film grids |
| Vitrification | |
| Details | Rapid-freezing in liquid ethane |
| Experiment | |
| Method | ELECTRON MICROSCOPY |
 Electron Microscopy | |
| Imaging | |
| Microscope | Model: FEI TECNAI F20 |
|---|---|
| Date | 2001-06-01 |
| Electron gun | |
| Electron source | FIELD EMISSION GUN |
| Accelerating voltage | 200 kV |
| Electron dose | 2000 e/A**2 |
| Illumination mode | FLOOD BEAM |
| Lens | |
| Mode | BRIGHT FIELD |
| Magnification | Calibrated: 49696 X, Nominal: 50000 X |
| Cs | Nominal: 2.0 mm |
| Nominal defocus | Max: 4000. nm, Min: 1500. nm |
| Specimen holder | |
| Tilt angle | Min: 0 degrees, Max: 0 degrees |
| Temperature | 93 Kelvin |
| Detector | |
| Type | KODAK SO163 FILM |
 Processing | |
| Single particle entity | |
| Symmetry type | ASYMMETRIC |
|---|---|
| 3D reconstruction | |
| Actual pixel size | 2.82 A/pix |
| CTF correction method | CTF correction of 3D-maps by Wiener filtration |
| Details | SPIDER package. CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS EF-G H573A AT 2.8A RESOLUTION. |
| Magnification calibration | TMV |
| Method | 3D projection matching; conjugate gradients with regularization |
| Resolution | 10.8 A |
| 3D fitting | |
| Method | Manual fitting in O |
| Refinement Space | REAL |
| 3D fitting list | |
| 3D fitting id | 1 |
| PDB entry ID | 1FNM |
| Refine hist | |
| Cycle id | LAST |
| Refine id | ELECTRON MICROSCOPY |
| Total atoms | 655 |
| Protein atoms | 655 |
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