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Structural characterization of mRNA-tRNA translocation intermediates (30S ribosome of class 5 of the six classes)
by single particle reconstruction, at 11.5 A resolution
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3j0z |
|---|---|
| Title | Structural characterization of mRNA-tRNA translocation intermediates (30S ribosome of class 5 of the six classes) |
| Descriptor | PROTEIN/RNA Complex |
| Keywords |  RIBOSOME, cryoelectron microscopy, molecular dynamics flexible fitting, ratchet-like rotation |
| Authors | Agirrezabala, X., Liao, H., Schreiner, E., Fu, J., Ortiz-Meoz, R.F., Schulten, K., Green, R., Frank, J. |
| Date | Deposition: 2011-12-08, Release: 2012-03-21 |
| 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-5363, Made by Jmol #3: With PDB-3j12, Made by Jmol #4: Superimposing with EM 3D map: EMDB-5363 (with PDB-3j12), 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 Split: split data constructing the same model |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - primary | |
| Article | Proc. Natl. Acad. Sci. U.S.A., Vol. 109, Issue 16, Page 6094-9, Year 2012 |
|---|---|
| Title | Structural characterization of mRNA-tRNA translocation intermediates. |
| Authors | Xabier Agirrezabala, Hstau Y Liao, Eduard Schreiner, Jie Fu, Rodrigo F Ortiz-Meoz, Klaus Schulten, Rachel Green, Joachim Frank Structural Biology Unit, CIC-bioGUNE, Bizkaia Technology Park, Derio 48160, Basque Country, Spain. |
| Keywords | Binding Sites, Cryoelectron Microscopy, Crystallography, X-Ray, Escherichia coli (genetics), Macromolecular Substances (chemistry), Models, Molecular, Molecular Conformation, Protein Biosynthesis, RNA, Messenger (genetics), RNA, Transfer (genetics, 9014-25-9), Ribosomes (metabolism), Thermodynamics |
| Links | DOI: 10.1073/pnas.1201288109, PubMed: 22467828, PMC: PMC3340995 |
 Components | |
| ID 1 : 16S ribosomal RNA | |
| Image |   |
|---|---|
| Description | 16S ribosomal RNA |
| Type | polymer |
| Formula weight | 499875.594 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli
|
| Links | GenBank: 83754040, Sequence view |
| ID 2 : A site tRNA | |
| Image |   |
| Description | A site tRNA |
| Type | polymer |
| Formula weight | 24645.086 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | Sequence view |
| ID 3 : mRNA | |
| Image |   |
| Description | mRNA |
| Type | polymer |
| Formula weight | 15036.932 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | Sequence view |
| ID 4 : P site tRNA | |
| Image |   |
| Description | P site tRNA |
| Type | polymer |
| Formula weight | 24833.076 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | Sequence view |
| ID 5 : 30S ribosomal protein S2 | |
| Image |   |
| Description | 30S ribosomal protein S2 |
| Type | polymer |
| Formula weight | 26650.656 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7V0, Sequence view |
| ID 6 : 30S ribosomal protein S3 | |
| Image |   |
| Description | 30S ribosomal protein S3 |
| Type | polymer |
| Formula weight | 25900.342 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7V3, Sequence view |
| ID 7 : 30S ribosomal protein S4 | |
| Image |   |
| Description | 30S ribosomal protein S4 |
| Type | polymer |
| Formula weight | 23383.191 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7V8, Sequence view |
| ID 8 : 30S ribosomal protein S5 | |
| Image |   |
| Description | 30S ribosomal protein S5 |
| Type | polymer |
| Formula weight | 17498.340 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7W1, Sequence view |
| ID 9 : 30S ribosomal protein S6 | |
| Image |   |
| Description | 30S ribosomal protein S6 |
| Type | polymer |
| Formula weight | 15727.645 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P02358, Sequence view |
| ID 10 : 30S ribosomal protein S7 | |
| Image |   |
| Description | 30S ribosomal protein S7 |
| Type | polymer |
| Formula weight | 19924.133 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P02359, Sequence view |
| ID 11 : 30S ribosomal protein S8 | |
| Image |   |
| Description | 30S ribosomal protein S8 |
| Type | polymer |
| Formula weight | 14015.469 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7W7, Sequence view |
| ID 12 : 30S ribosomal protein S9 | |
| Image |   |
| Description | 30S ribosomal protein S9 |
| Type | polymer |
| Formula weight | 14755.199 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7X3, Sequence view |
| ID 13 : 30S ribosomal protein S10 | |
| Image |   |
| Description | 30S ribosomal protein S10 |
| Type | polymer |
| Formula weight | 11755.708 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7R5, Sequence view |
| ID 14 : 30S ribosomal protein S11 | |
| Image |   |
| Description | 30S ribosomal protein S11 |
| Type | polymer |
| Formula weight | 13739.899 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7R9, Sequence view |
| ID 15 : 30S ribosomal protein S12 | |
| Image |   |
| Description | 30S ribosomal protein S12 |
| Type | polymer |
| Formula weight | 13637.070 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7S3, Sequence view |
| ID 16 : 30S ribosomal protein S13 | |
| Image |   |
| Description | 30S ribosomal protein S13 |
| Type | polymer |
| Formula weight | 12997.379 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7S9, Sequence view |
| ID 17 : 30S ribosomal protein S14 | |
| Image |   |
| Description | 30S ribosomal protein S14 |
| Type | polymer |
| Formula weight | 11475.461 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AG59, Sequence view |
| ID 18 : 30S ribosomal protein S15 | |
| Image |   |
| Description | 30S ribosomal protein S15 |
| Type | polymer |
| Formula weight | 10188.777 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: Q8X9M2, Sequence view |
| ID 19 : 30S ribosomal protein S16 | |
| Image |   |
| Description | 30S ribosomal protein S16 |
| Type | polymer |
| Formula weight | 9207.662 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7T3, Sequence view |
| ID 20 : 30S ribosomal protein S17 | |
| Image |   |
| Description | 30S ribosomal protein S17 |
| Type | polymer |
| Formula weight | 9593.380 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AG63, Sequence view |
| ID 21 : 30S ribosomal protein S18 | |
| Image |   |
| Description | 30S ribosomal protein S18 |
| Type | polymer |
| Formula weight | 8874.362 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7T7, Sequence view |
| ID 22 : 30S ribosomal protein S19 | |
| Image |   |
| Description | 30S ribosomal protein S19 |
| Type | polymer |
| Formula weight | 10324.260 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7U3, Sequence view |
| ID 23 : 30S ribosomal protein S20 | |
| Image |   |
| Description | 30S ribosomal protein S20 |
| Type | polymer |
| Formula weight | 9577.354 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7U7, Sequence view |
| ID 24 : 30S ribosomal protein S21 | |
| Image |   |
| Description | 30S ribosomal protein S21 |
| Type | polymer |
| Formula weight | 8392.929 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P68679, Sequence view |
| ID 25 : TRYPTOPHAN | |
| Image |    |
| Description | TRYPTOPHAN |
| Type | non-polymer |
| Formula weight | 204.228 Da |
| Number of molecules | 1 |
| Source | Method: Obtained synthetically |
| ID 26 : N-FORMYLMETHIONINE | |
| Image |    |
| Description | N-FORMYLMETHIONINE |
| Type | non-polymer |
| Formula weight | 177.218 Da |
| Number of molecules | 1 |
| Source | Method: Obtained synthetically |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Mass-estimation Method | 2.8 |
| Theoretical Mass | 2.8 |
| Name | Trp-tRNA-EFTu-GDP-kir-70S ribosome |
| Num components | 3 |
| Entity assembly | |
| Details | with A and P site tRNAs |
| Name | 70S ribosome |
| Type | RIBOSOME |
| Buffer | |
| Name | HiFi buffer (50 mM Tris-HCl, pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2) |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| pH | 7.5 |
| Sample concentration | 0.03 mg/ml |
| Sample support | |
| Details | 200 mesh |
| Grid mesh size | 200 |
| Vitrification | |
| Cryogen name | NITROGEN |
| Details | Blot for 3 seconds, plunge into liquid nitrogen (Vitrobot) |
| Humidity | 90 |
| Instrument | Vitrobot |
| Method | blot for 3 seconds |
| Temp | 80 Kelvin |
 Electron Microscopy | |
| Imaging | |
| Microscope | model: FEI TECNAI F30 |
|---|---|
| Date | 2011-05-01 |
| Details | automated data collection system AutoEMation (CCD mag. 100000x) |
| Electron gun | |
| Electron source | FIELD EMISSION GUN |
| Accelerating voltage | 300 kV |
| Electron dose | 25 e/A**2 |
| Illumination mode | FLOODBEAM |
| Lens | |
| Mode | BRIGHTFIELD |
| Magnification | calibrated: 58269 X, nominal: 59000 X |
| Cs | nominal: 2.26 mm |
| Nominal defocus | max: 4000 nm, min: 1200 nm |
| Energy filter | none |
| Specimen holder | |
| Specimen holder | model: OTHER, type: cartridge |
| Temperature | 80.7 Kelvin |
| Recording temperature | maximum: 80.7, minimum: 80.7 |
| Detector | |
| Type | TVIPS TemCam-F415 (CCD) |
 Processing | |
| 2D projection selection | |
| Number of particles | 40000 |
|---|---|
| Software name | MDFF |
| Single particle entity | |
| Symmetry type | ASYMMETRIC |
| 3D reconstruction | |
| Actual pixel size | 1.5 A/pix |
| CTF correction method | Volumes were CTF-corrected in defocus groups |
| Magnification calibration | 50000 |
| Number of particles | 40000 |
| Resolution | 11.5 A |
| Resolution method | FSC at 0.5 cut-off |
| Software | SPIDER |
| 3D fitting | |
| Refinement Protocol | Molecular Dynamics based flexible fitting |
| Refinement Space | REAL |
| Software name | MDFF |
| Target criteria | RMSD, cross correlation |
| 3D fitting list | |
| PDB entry ID | 2I2U |
| Refine hist | |
| Total atoms | 57562 |
| Ligand atoms | 24 |
| Nucleic acid atoms | 37350 |
| Protein atoms | 20188 |
 Download | |||
| PDB format | |||
| All | pdb3j0z.ent.gzpdb3j0z.ent (uncompressed file) | ||
|---|---|---|---|
| Header only | pdb3j0z.ent.gz | ||
| mmCIF format | |||
| mmCIF | 3j0z.cif.gz | ||
| XML format | |||
| All | 3j0z.xml.gz | ||
| No-atom | 3j0z-noatom.xml.gz | ||
| Ext-atom | 3j0z-extatom.xml.gz | ||
| Movie files | |||
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