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Structure of the bacterial ribosome complexed by tmRNA-SmpB and EF-G during translocation and MLD-loading (30S subunit)
by single particle reconstruction, at 8.3 A resolution
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3j18 |
|---|---|
| Title | Structure of the bacterial ribosome complexed by tmRNA-SmpB and EF-G during translocation and MLD-loading (30S subunit) |
| Descriptor | PROTEIN/RNA Complex |
| Keywords |  RIBOSOME, trans-translation, MLD-loading, translocation |
| Authors | Ramrath, D.J.F., Yamamoto, H., Rother, K., Wittek, D., Pech, M., Mielke, T., Loerke, J., Scheerer, P., Ivanov, P., Teraoka, Y., Shpanchenko, O., Nierhaus, K.H., Spahn, C.M.T. |
| Date | Deposition: 2012-01-27, Release: 2012-05-09 |
| PDBj Mine pages |  Summary, Structural Details, Experimental Details, Functional Details |
| Other databases | RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST |
| Sequence details | MODELED SEQUENCES FOR SSRA_BINDING PROTEIN (UNP Q8RR57 RESIDUES 1-123) AND ELONGATION FACTOR G (UNP Q5SHN5 1-691) ARE FROM THERMUS THERMOPHILUS. |
| Structure Visualization | |
| Movies |  Movie Page#1: Depositted structure unit, Made by Jmol #2: Superimposing with simplified surface model of EM map, EMDB-5386, Made by Jmol #3: With PDB-3j19, Made by Jmol #4: Superimposing with EM 3D map: EMDB-5386 (with PDB-3j19), 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 | Nature, Vol. 485, Issue 7399, Page 526-9, Year 2012 |
|---|---|
| Title | The complex of tmRNA-SmpB and EF-G on translocating ribosomes. |
| Authors | David J F Ramrath, Hiroshi Yamamoto, Kristian Rother, Daniela Wittek, Markus Pech, Thorsten Mielke, Justus Loerke, Patrick Scheerer, Pavel Ivanov, Yoshika Teraoka, Olga Shpanchenko, Knud H Nierhaus, Christian M T Spahn Institut für Medizinische Physik und Biophysik, Charite - Universitätsmedizin Berlin, Ziegelstrasse 5-9, 10117 Berlin, Germany. |
| Keywords | Base Sequence, Cryoelectron Microscopy, Escherichia coli (chemistry), Fusidic Acid (metabolism, 6990-06-3), Ligands, Models, Molecular, Nucleic Acid Conformation, Peptide Elongation Factor G (chemistry), Protein Binding, Protein Biosynthesis, Protein Conformation, RNA, Bacterial (chemistry), RNA-Binding Proteins (chemistry), Ribosome Subunits (chemistry), Ribosomes (chemistry), small protein B, tmRNA |
| Links | DOI: 10.1038/nature11006, PubMed: 22622583 |
 Components | |
| ID 1 : 16S ribosomal RNA | |
| Image |   |
|---|---|
| Description | 16S ribosomal RNA |
| Type | polymer |
| Formula weight | 498726.594 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli
Strain: CAN20 |
| Links | GenBank: NC_000913, Sequence view |
| ID 2 : 30S ribosomal protein S2 | |
| Image |   |
| Description | 30S ribosomal protein S2 |
| Type | polymer |
| Formula weight | 24254.115 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: CAN20 |
| Links | UniProt: P0A7V0, Sequence view |
| ID 3 : 30S ribosomal protein S3 | |
| Image |   |
| Description | 30S ribosomal protein S3 |
| Type | polymer |
| Formula weight | 23078.988 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: CAN20 |
| Links | UniProt: P0A7V3, Sequence view |
| ID 4 : 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 Strain: CAN20 |
| Links | UniProt: P0A7V8, Sequence view |
| ID 5 : 30S ribosomal protein S5 | |
| Image |   |
| Description | 30S ribosomal protein S5 |
| Type | polymer |
| Formula weight | 15804.407 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: CAN20 |
| Links | UniProt: P0A7W1, Sequence view |
| ID 6 : 30S ribosomal protein S6 | |
| Image |   |
| Description | 30S ribosomal protein S6 |
| Type | polymer |
| Formula weight | 11669.469 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: CAN20 |
| Links | UniProt: P02358, Sequence view |
| ID 7 : 30S ribosomal protein S7 | |
| Image |   |
| Description | 30S ribosomal protein S7 |
| Type | polymer |
| Formula weight | 16861.672 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: CAN20 |
| Links | UniProt: P02359, Sequence view |
| ID 8 : 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 Strain: CAN20 |
| Links | UniProt: P0A7W7, Sequence view |
| ID 9 : 30S ribosomal protein S9 | |
| Image |   |
| Description | 30S ribosomal protein S9 |
| Type | polymer |
| Formula weight | 14555.005 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: CAN20 |
| Links | UniProt: P0A7X3, Sequence view |
| ID 10 : 30S ribosomal protein S10 | |
| Image |   |
| Description | 30S ribosomal protein S10 |
| Type | polymer |
| Formula weight | 11197.099 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: CAN20 |
| Links | UniProt: P0A7R5, Sequence view |
| ID 11 : 30S ribosomal protein S11 | |
| Image |   |
| Description | 30S ribosomal protein S11 |
| Type | polymer |
| Formula weight | 12487.310 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: CAN20 |
| Links | UniProt: P0A7R9, Sequence view |
| ID 12 : 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 Strain: CAN20 |
| Links | UniProt: P0A7S3, Sequence view |
| ID 13 : 30S ribosomal protein S13 | |
| Image |   |
| Description | 30S ribosomal protein S13 |
| Type | polymer |
| Formula weight | 12625.857 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: CAN20 |
| Links | UniProt: P0A7S9, Sequence view |
| ID 14 : 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 Strain: CAN20 |
| Links | UniProt: P0AG59, Sequence view |
| ID 15 : 30S ribosomal protein S15 | |
| Image |   |
| Description | 30S ribosomal protein S15 |
| Type | polymer |
| Formula weight | 10159.713 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: CAN20 |
| Links | UniProt: P0ADZ4, Sequence view |
| ID 16 : 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 Strain: CAN20 |
| Links | UniProt: P0A7T3, Sequence view |
| ID 17 : 30S ribosomal protein S17 | |
| Image |   |
| Description | 30S ribosomal protein S17 |
| Type | polymer |
| Formula weight | 9264.026 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: CAN20 |
| Links | UniProt: P0AG63, Sequence view |
| ID 18 : 30S ribosomal protein S18 | |
| Image |   |
| Description | 30S ribosomal protein S18 |
| Type | polymer |
| Formula weight | 6466.543 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: CAN20 |
| Links | UniProt: P0A7T7, Sequence view |
| ID 19 : 30S ribosomal protein S19 | |
| Image |   |
| Description | 30S ribosomal protein S19 |
| Type | polymer |
| Formula weight | 9057.713 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: CAN20 |
| Links | UniProt: P0A7U3, Sequence view |
| ID 20 : 30S ribosomal protein S20 | |
| Image |   |
| Description | 30S ribosomal protein S20 |
| Type | polymer |
| Formula weight | 9506.276 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: CAN20 |
| Links | UniProt: P0A7U7, Sequence view |
| ID 21 : 30S ribosomal protein S21 | |
| Image |   |
| Description | 30S ribosomal protein S21 |
| Type | polymer |
| Formula weight | 6067.142 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: CAN20 |
| Links | UniProt: P68679, Sequence view |
| ID 22 : full length transfer messenger RNA (tmRNA) | |
| Image |   |
| Description | full length transfer messenger RNA (tmRNA) |
| Type | polymer |
| Formula weight | 117213.414 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | GenBank: NC_000913, Sequence view |
| ID 23 : SsrA-binding protein | |
| Image |   |
| Description | SsrA-binding protein |
| Type | polymer |
| Fragment | SEE REMARK 999 |
| Formula weight | 14177.613 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a genetically manipulated source Gene: ID:562, Escherichia coliHost: ID:511693, Escherichia coli, BL21, plasmidPlasmid name: pGEMEX-2 |
| Links | Sequence view |
| ID 24 : formyl-methionine specific initiator transfer RNA | |
| Image |   |
| Description | formyl-methionine specific initiator transfer RNA |
| Type | polymer |
| Formula weight | 24802.943 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | GenBank: NC_000913, Sequence view |
| ID 25 : EF-G | |
| Image |   |
| Description | elongation factor G |
| Type | polymer |
| Fragment | SEE REMARK 999 |
| Formula weight | 76977.914 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a genetically manipulated source Gene: ID:562, Escherichia coliHost: ID:511693, Escherichia coli, BL21, plasmidPlasmid name: pET-28 |
| Links | Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Details | in vitro reconstituted ribosomal complex |
| Name | Ribosomal complex 70S-tmRNA-SmpB-tRNA-EFG-GDP-FA |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| pH | 7.6 |
| Sample concentration | 0.15 mg/ml |
| Sample support | |
| Details | Quantifoil R3-3 Cu mesh with 2 nm carbon support film |
| Vitrification | |
| Cryogen name | ETHANE |
| Details | blot for 5-10 seconds before plunging into liquid ethane (FEI Vitrobot) |
| Humidity | 100 |
| Instrument | FEI Vitrobot |
| Method | blot for 5-10 seconds before plunging |
| Temp | 96.15 Kelvin |
 Electron Microscopy | |
| Imaging | |
| Microscope | model: FEI POLARA 300 |
|---|---|
| Date | 2009-12-08 |
| Electron gun | |
| Electron source | Field Emission Gun |
| Accelerating voltage | 300 kV |
| Electron dose | 20 e/A**2 |
| Illumination mode | SPOTSCAN |
| Lens | |
| Mode | BRIGHTFIELD |
| Magnification | calibrated: 39000 X, nominal: 39000 X |
| Cs | nominal: 2.0 mm |
| Nominal defocus | max: 5000 nm, min: 2500 nm |
| Specimen holder | |
| Temperature | 77 Kelvin |
| Detector | |
| Type | KODAK SO163 FILM |
| Image scans | |
| Number digital images | 302 |
 Processing | |
| 2D projection selection | |
| Number of particles | 68843 |
|---|---|
| Single particle entity | |
| Symmetry type | ASYMMETRIC |
| 3D reconstruction | |
| Actual pixel size | 1.26 A/pix |
| CTF correction method | The volumes were CTF-corrected in defocus groups, with an average of approximately 215 individual images per group |
| Method | angular refinement |
| Nominal pixel size | 1.26 A/pix |
| Number of particles | 68843 |
| Resolution | 8.3 A |
| Software | SPIDER |
| Refine hist | |
| Total atoms | 66532 |
| Nucleic acid atoms | 41770 |
| Protein atoms | 24762 |
 Download | |||
| PDB format | |||
| All | pdb3j18.ent.gzpdb3j18.ent (uncompressed file) | ||
|---|---|---|---|
| Header only | pdb3j18.ent.gz | ||
| mmCIF format | |||
| mmCIF | 3j18.cif.gz | ||
| XML format | |||
| All | 3j18.xml.gz | ||
| No-atom | 3j18-noatom.xml.gz | ||
| Ext-atom | 3j18-extatom.xml.gz | ||
| Movie files | |||
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