3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Structural characterization of mRNA-tRNA translocation intermediates (50S ribosome of class 6 of the six classes)
by single particle reconstruction, at 11.5 A resolution
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3j14 |
|---|---|
| Title | Structural characterization of mRNA-tRNA translocation intermediates (50S ribosome of class 6 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: 2011-12-09, 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-5362, Made by Jmol #3: With PDB-3j10, Made by Jmol #4: Superimposing with EM 3D map: EMDB-5362 (with PDB-3j10), 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 : 5S ribomosomal RNA | |
| Image |   |
|---|---|
| Description | 5S ribomosomal RNA |
| Type | polymer |
| Formula weight | 38790.309 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli
|
| Links | GenBank: 33357928, Sequence view |
| ID 2 : 23S ribomosomal RNA | |
| Image |   |
| Description | 23S ribomosomal RNA |
| Type | polymer |
| Formula weight | 941814.875 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | GenBank: 33357927, Sequence view |
| ID 3 : 50S ribosomal protein L1 | |
| Image |   |
| Description | 50S ribosomal protein L1 |
| Type | polymer |
| Formula weight | 24765.834 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:2285Organism scientific: Sulfolobus acidocaldarius |
| Links | UniProt: P0A7L0, Sequence view |
| ID 4 : 50S ribosomal protein L2 | |
| Image |   |
| Description | 50S ribosomal protein L2 |
| Type | polymer |
| Formula weight | 29792.650 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P60422, Sequence view |
| ID 5 : 50S ribosomal protein L3 | |
| Image |   |
| Description | 50S ribosomal protein L3 |
| Type | polymer |
| Formula weight | 22277.709 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P60438, Sequence view |
| ID 6 : 50S ribosomal protein L4 | |
| Image |   |
| Description | 50S ribosomal protein L4 |
| Type | polymer |
| Formula weight | 22121.723 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P60723, Sequence view |
| ID 7 : 50S ribosomal protein L5 | |
| Image |   |
| Description | 50S ribosomal protein L5 |
| Type | polymer |
| Formula weight | 20202.566 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P62399, Sequence view |
| ID 8 : 50S ribosomal protein L6 | |
| Image |   |
| Description | 50S ribosomal protein L6 |
| Type | polymer |
| Formula weight | 18801.766 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AG55, Sequence view |
| ID 9 : 50S ribosomal protein L9 | |
| Image |   |
| Description | 50S ribosomal protein L9 |
| Type | polymer |
| Formula weight | 15789.174 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7R1, Sequence view |
| ID 10 : 50S ribosomal protein L10 | |
| Image |   |
| Description | 50S ribosomal protein L10 |
| Type | polymer |
| Formula weight | 17605.537 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:2285Organism scientific: Sulfolobus acidocaldarius |
| Links | UniProt: P0A7J3, Sequence view |
| ID 11 : 50S ribosomal protein L11 | |
| Image |   |
| Description | 50S ribosomal protein L11 |
| Type | polymer |
| Formula weight | 14763.286 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7J7, Sequence view |
| ID 12 : 50S ribosomal protein L13 | |
| Image |   |
| Description | 50S ribosomal protein L13 |
| Type | polymer |
| Formula weight | 16050.749 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AA10, Sequence view |
| ID 13 : 50S ribosomal protein L14 | |
| Image |   |
| Description | 50S ribosomal protein L14 |
| Type | polymer |
| Formula weight | 13565.172 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0ADY3, Sequence view |
| ID 14 : 50S ribosomal protein L15 | |
| Image |   |
| Description | 50S ribosomal protein L15 |
| Type | polymer |
| Formula weight | 15008.598 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P02413, Sequence view |
| ID 15 : 50S ribosomal protein L16 | |
| Image |   |
| Description | 50S ribosomal protein L16 |
| Type | polymer |
| Formula weight | 15312.394 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0ADY7, Sequence view |
| ID 16 : 50S ribosomal protein L17 | |
| Image |   |
| Description | 50S ribosomal protein L17 |
| Type | polymer |
| Formula weight | 14393.774 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AG44, Sequence view |
| ID 17 : 50S ribosomal protein L18 | |
| Image |   |
| Description | 50S ribosomal protein L18 |
| Type | polymer |
| Formula weight | 12794.793 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0C018, Sequence view |
| ID 18 : 50S ribosomal protein L19 | |
| Image |   |
| Description | 50S ribosomal protein L19 |
| Type | polymer |
| Formula weight | 13028.207 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7K6, Sequence view |
| ID 19 : 50S ribosomal protein L20 | |
| Image |   |
| Description | 50S ribosomal protein L20 |
| Type | polymer |
| Formula weight | 13396.962 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7L3, Sequence view |
| ID 20 : 50S ribosomal protein L21 | |
| Image |   |
| Description | 50S ribosomal protein L21 |
| Type | polymer |
| Formula weight | 11586.485 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AG48, Sequence view |
| ID 21 : 50S ribosomal protein L22 | |
| Image |   |
| Description | 50S ribosomal protein L22 |
| Type | polymer |
| Formula weight | 12253.464 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P61175, Sequence view |
| ID 22 : 50S ribosomal protein L23 | |
| Image |   |
| Description | 50S ribosomal protein L23 |
| Type | polymer |
| Formula weight | 11222.270 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0ADZ0, Sequence view |
| ID 23 : 50S ribosomal protein L24 | |
| Image |   |
| Description | 50S ribosomal protein L24 |
| Type | polymer |
| Formula weight | 11208.169 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P60624, Sequence view |
| ID 24 : 50S ribosomal protein L25 | |
| Image |   |
| Description | 50S ribosomal protein L25 |
| Type | polymer |
| Formula weight | 10713.566 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P68919, Sequence view |
| ID 25 : 50S ribosomal protein L27 | |
| Image |   |
| Description | 50S ribosomal protein L27 |
| Type | polymer |
| Formula weight | 9015.426 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7L8, Sequence view |
| ID 26 : 50S ribosomal protein L28 | |
| Image |   |
| Description | 50S ribosomal protein L28 |
| Type | polymer |
| Formula weight | 8896.435 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7M2, Sequence view |
| ID 27 : 50S ribosomal protein L29 | |
| Image |   |
| Description | 50S ribosomal protein L29 |
| Type | polymer |
| Formula weight | 7286.531 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7M6, Sequence view |
| ID 28 : 50S ribosomal protein L30 | |
| Image |   |
| Description | 50S ribosomal protein L30 |
| Type | polymer |
| Formula weight | 6423.682 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AG51, Sequence view |
| ID 29 : 50S ribosomal protein L31 | |
| Image |   |
| Description | 50S ribosomal protein L31 |
| Type | polymer |
| Formula weight | 7887.165 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7M9, Sequence view |
| ID 30 : 50S ribosomal protein L32 | |
| Image |   |
| Description | 50S ribosomal protein L32 |
| Type | polymer |
| Formula weight | 6332.307 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7N4, Sequence view |
| ID 31 : 50S ribosomal protein L33 | |
| Image |   |
| Description | 50S ribosomal protein L33 |
| Type | polymer |
| Formula weight | 6257.510 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7N9, Sequence view |
| ID 32 : 50S ribosomal protein L34 | |
| Image |   |
| Description | 50S ribosomal protein L34 |
| Type | polymer |
| Formula weight | 5397.506 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7P5, Sequence view |
| ID 33 : 50S ribosomal protein L35 | |
| Image |   |
| Description | 50S ribosomal protein L35 |
| Type | polymer |
| Formula weight | 7181.907 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7Q1, Sequence view |
| ID 34 : 50S ribosomal protein L36 | |
| Image |   |
| Description | 50S ribosomal protein L36 |
| Type | polymer |
| Formula weight | 4377.415 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7Q6, Sequence view |
 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 | 37000 |
|---|---|
| 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 | 37000 |
| 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 | 2I2V |
| Refine hist | |
| Total atoms | 94789 |
| Nucleic acid atoms | 64917 |
| Protein atoms | 29872 |
 Download | |||
| PDB format | |||
| All | pdb3j14.ent.gzpdb3j14.ent (uncompressed file) | ||
|---|---|---|---|
| Header only | pdb3j14.ent.gz | ||
| mmCIF format | |||
| mmCIF | 3j14.cif.gz | ||
| XML format | |||
| All | 3j14.xml.gz | ||
| No-atom | 3j14-noatom.xml.gz | ||
| Ext-atom | 3j14-extatom.xml.gz | ||
| Movie files | |||
| movie #1 |
| ||
| movie #2 |
| ||
| movie #3 |
| ||
| movie #4 |
| ||
Top
Gallery
List
Diagram
Statistics
Documents
PDBj
EM Navigator
Detail page - PDB-3j14
Contact