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Models for the T. thermophilus ribosome recycling factor bound to the E. coli post-termination complex
by single particle reconstruction, at 11.1 A resolution
#1: Depositted structure unit, Made by Jmol
#2: Superimposing with simplified surface model of EM map, EMDB-1915, Made by Jmol
#3: Superimposing with simplified surface model of EM map, EMDB-1916, Made by Jmol
#4: Superimposing with EM 3D map: EMDB-1915, Made by UCSF CHIMERA
#5: Superimposing with EM 3D map: EMDB-1916, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3j0d |
|---|---|
| Title | Models for the T. thermophilus ribosome recycling factor bound to the E. coli post-termination complex |
| Descriptor | PROTEIN/RNA Complex |
| Keywords |  TRANSLATION, ribosome, ribosome recycling factor |
| Authors | Yokoyama, T., Shaikh, T.R., Iwakura, N., Kaji, H., Kaji, A., Agrawal, R.K. |
| Date | Deposition: 2011-06-29, Release: 2012-04-25 |
| PDBj Mine pages |  Summary, Structural Details, Experimental Details, Functional Details |
| Other databases | RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST |
| Sequence details | RIBOSOMAL RNA IS ONLY PARTIALLY MODELED IN THIS ENTRY: CHAINS A-F ARE PARTS OF THE 23S RIBOSOMAL RNA AND CHAINS H AND h ARE PARTS OF THE 16S RIBOSOMAL RNA. |
| Structure Visualization | |
| Movies |  Movie Page#1: Depositted structure unit, Made by Jmol #2: Superimposing with simplified surface model of EM map, EMDB-1915, Made by Jmol #3: Superimposing with simplified surface model of EM map, EMDB-1916, Made by Jmol #4: Superimposing with EM 3D map: EMDB-1915, Made by UCSF CHIMERA #5: Superimposing with EM 3D map: EMDB-1916, Made by UCSF CHIMERA |
| Structure viewers |  Yorodumi, jV4, Jmol,  Biological unit (Images, jV) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: target map of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - primary | |
| Article | EMBO J., Vol. 31, Issue 7, Page 1836-46, Year 2012 |
|---|---|
| Title | Structural insights into initial and intermediate steps of the ribosome-recycling process. |
| Authors | Takeshi Yokoyama, Tanvir R Shaikh, Nobuhiro Iwakura, Hideko Kaji, Akira Kaji, Rajendra K Agrawal Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY, USA. |
| Keywords | Cryoelectron Microscopy, Escherichia coli (metabolism), Escherichia coli Proteins (metabolism), L11 protein, E coli, Peptide Elongation Factor G (metabolism), Protein Binding, Protein Conformation, RNA, Ribosomal (metabolism), Ribosomal Proteins (metabolism), Ribosomes (metabolism), ribosome releasing factor |
| Links | DOI: 10.1038/emboj.2012.22, PubMed: 22388519, PMC: PMC3321202 |
 Components | |
| ID 1 : ribosomal 23S RNA | |
| Image |   |
|---|---|
| Description | ribosomal 23S RNA |
| Type | polyribonucleotide |
| Fragment | helices 43 and 44 |
| Formula weight | 16114.751 Da |
| Number of molecules | 1 |
| ID | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli
|
| Links | GenBank: U00096.2, Sequence view |
| ID 2 : ribosomal 23S RNA | |
| Image |   |
| Description | ribosomal 23S RNA |
| Type | polyribonucleotide |
| Fragment | helix 69 |
| Formula weight | 6994.250 Da |
| Number of molecules | 1 |
| ID | 2 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | GenBank: U00096.2, Sequence view |
| ID 3 : ribosomal 23S RNA | |
| Image |   |
| Description | ribosomal 23S RNA |
| Type | polyribonucleotide |
| Fragment | helix 71 |
| Formula weight | 5459.323 Da |
| Number of molecules | 1 |
| ID | 3 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | GenBank: U00096.2, Sequence view |
| ID 4 : ribosomal 23S RNA | |
| Image |   |
| Description | ribosomal 23S RNA |
| Type | polyribonucleotide |
| Fragment | helix 80 |
| Formula weight | 4228.593 Da |
| Number of molecules | 1 |
| ID | 4 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | GenBank: U00096.2, Sequence view |
| ID 5 : ribosomal 23S RNA | |
| Image |   |
| Description | ribosomal 23S RNA |
| Type | polyribonucleotide |
| Fragment | helix 93 |
| Formula weight | 6117.740 Da |
| Number of molecules | 1 |
| ID | 5 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | GenBank: U00096.2, Sequence view |
| ID 6 : ribosomal 23S RNA | |
| Image |   |
| Description | ribosomal 23S RNA |
| Type | polyribonucleotide |
| Fragment | helix 95 |
| Formula weight | 6155.794 Da |
| Number of molecules | 1 |
| ID | 6 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | GenBank: U00096.2, Sequence view |
| ID 7 : 50S ribosomal protein L11 | |
| Image |   |
| Description | 50S ribosomal protein L11 |
| Type | polypeptide(L) |
| Formula weight | 14763.286 Da |
| Number of molecules | 1 |
| ID | 7 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7J7, Sequence view |
| ID 8 : ribosomal 16S RNA | |
| Image |   |
| Description | ribosomal 16S RNA |
| Type | polyribonucleotide |
| Fragment | helix 44 strand 1 |
| Formula weight | 5787.546 Da |
| Number of molecules | 1 |
| ID | 8 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | GenBank: U00096.2, Sequence view |
| ID 9 : ribosomal 16S RNA | |
| Image |   |
| Description | ribosomal 16S RNA |
| Type | polypeptide(L) |
| Fragment | helix 44 strand 2 |
| Formula weight | 6173.764 Da |
| Number of molecules | 1 |
| ID | 9 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | GenBank: U00096.2, Sequence view |
| ID 10 : 30S ribosomal protein S12 | |
| Image |   |
| Description | 30S ribosomal protein S12 |
| Type | polypeptide(L) |
| Formula weight | 13637.070 Da |
| Number of molecules | 1 |
| ID | 10 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7S3, Sequence view |
| ID 11 : RRF, Ribosome-releasing factor | |
| Image |   |
| Description | Ribosome-recycling factor |
| Type | polyribonucleotide |
| Formula weight | 21029.262 Da |
| Number of molecules | 1 |
| ID | 11 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: Q9WX76, Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Details | POTC-TTRRF |
| Name | E. COLI POST TERMINATION COMPLEX |
| Buffer | |
| Name | BUFFER R |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| pH | 7.50 |
| Sample concentration | 0.08 mg/ml |
| Sample support | |
| Details | QUANTIFOIL HOLEY CARBON FILM G |
| Vitrification | |
| Details | VITROBOT |
| Experiment | |
| Method | ELECTRON MICROSCOPY |
 Electron Microscopy | |
| Imaging | |
| Microscope | Model: TECNAI F20 |
|---|---|
| Date | 2010-12-23 |
| Electron gun | |
| Electron source | FIELD EMISSION GUN |
| Accelerating voltage | 200 kV |
| Lens | |
| Magnification | Calibrated: 50310 X, Nominal: 50000 X |
| Nominal defocus | Max: 4300.00 nm, Min: 400.00 nm |
| Specimen holder | |
| Tilt angle | Min: 0.00 degrees, Max: 0.00 degrees |
| Temperature | 93.00 Kelvin |
| Detector | |
| Type | KODAK S0163 FILM |
 Processing | |
| 2D projection selection | |
| Number of particles | 153927 |
|---|---|
| Software name | SPIDER |
| Single particle entity | |
| Symmetry type | ASYMMETRIC |
| 3D reconstruction | |
| CTF correction method | CTF CORRECTION OF 3D MAPS BY WIENER FILTRATION |
| Method | 3D PROJECTION MATCHING |
| Nominal pixel size | 2.78 A/pix |
| Resolution | 11.1 A |
| 3D fitting | |
| Refinement Protocol | FLEXIBLE FITTING (MDFF) |
| 3D fitting list | |
| 3D fitting id | 1 |
| PDB entry ID | PDB ID 2AVY, 2AW4, 1EH1 |
| Refine hist | |
| Cycle id | LAST |
| Refine id | ELECTRON MICROSCOPY |
| Total atoms | 7260 |
| Nucleic acid atoms | 3796 |
| Protein atoms | 3464 |
 Download | |||
| PDB format | |||
| All | pdb3j0d.ent.gzpdb3j0d.ent (uncompressed file) | ||
|---|---|---|---|
| Header only | pdb3j0d.ent.gz | ||
| mmCIF format | |||
| mmCIF | 3j0d.cif.gz | ||
| XML format | |||
| All | 3j0d.xml.gz | ||
| No-atom | 3j0d-noatom.xml.gz | ||
| Ext-atom | 3j0d-extatom.xml.gz | ||
| Movie files | |||
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