[English] 日本語
Yorodumi- PDB-5afi: 2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5afi | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | 2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EM | ||||||||||||
Components |
| ||||||||||||
Keywords | RIBOSOME / TRANSLATION / PROTEIN SYNTHESIS / DECODING / ELONGATION FACTOR TU / TRNA / RNA MODIFICATION / ANTIBIOTIC | ||||||||||||
Function / homology | Function and homology information guanyl-nucleotide exchange factor complex / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / translational elongation / RNA folding ...guanyl-nucleotide exchange factor complex / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / translational elongation / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translation elongation factor activity / four-way junction DNA binding / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||
Authors | Fischer, N. / Neumann, P. / Konevega, A.L. / Bock, L.V. / Ficner, R. / Rodnina, M.V. / Stark, H. | ||||||||||||
Citation | Journal: Nature / Year: 2015 Title: Structure of the E. coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM. Authors: Niels Fischer / Piotr Neumann / Andrey L Konevega / Lars V Bock / Ralf Ficner / Marina V Rodnina / Holger Stark / Abstract: Single particle electron cryomicroscopy (cryo-EM) has recently made significant progress in high-resolution structure determination of macromolecular complexes due to improvements in electron ...Single particle electron cryomicroscopy (cryo-EM) has recently made significant progress in high-resolution structure determination of macromolecular complexes due to improvements in electron microscopic instrumentation and computational image analysis. However, cryo-EM structures can be highly non-uniform in local resolution and all structures available to date have been limited to resolutions above 3 Å. Here we present the cryo-EM structure of the 70S ribosome from Escherichia coli in complex with elongation factor Tu, aminoacyl-tRNA and the antibiotic kirromycin at 2.65-2.9 Å resolution using spherical aberration (Cs)-corrected cryo-EM. Overall, the cryo-EM reconstruction at 2.9 Å resolution is comparable to the best-resolved X-ray structure of the E. coli 70S ribosome (2.8 Å), but provides more detailed information (2.65 Å) at the functionally important ribosomal core. The cryo-EM map elucidates for the first time the structure of all 35 rRNA modifications in the bacterial ribosome, explaining their roles in fine-tuning ribosome structure and function and modulating the action of antibiotics. We also obtained atomic models for flexible parts of the ribosome such as ribosomal proteins L9 and L31. The refined cryo-EM-based model presents the currently most complete high-resolution structure of the E. coli ribosome, which demonstrates the power of cryo-EM in structure determination of large and dynamic macromolecular complexes. | ||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5afi.cif.gz | 6.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5afi.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5afi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5afi_validation.pdf.gz | 897 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5afi_full_validation.pdf.gz | 1020.9 KB | Display | |
Data in XML | 5afi_validation.xml.gz | 167.6 KB | Display | |
Data in CIF | 5afi_validation.cif.gz | 288.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/5afi ftp://data.pdbj.org/pub/pdb/validation_reports/af/5afi | HTTPS FTP |
-Related structure data
Related structure data | 2847MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-RNA chain , 6 types, 7 molecules avwxyAB
#1: RNA chain | Mass: 498909.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: GenBank: 309700213 | ||||||||
---|---|---|---|---|---|---|---|---|---|
#22: RNA chain | Mass: 24818.893 Da / Num. of mol.: 2 / Fragment: Residues 49-125 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: GenBank: 147949 #23: RNA chain | | Mass: 3492.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 #24: RNA chain | | Mass: 24797.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 #26: RNA chain | | Mass: 941521.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0CE48*PLUS #27: RNA chain | | Mass: 38813.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 |
-30S ribosomal protein ... , 20 types, 20 molecules bcdefghijklmnopqrstu
#2: Protein | Mass: 26652.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7V0 |
---|---|
#3: Protein | Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7V3 |
#4: Protein | Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7V8 |
#5: Protein | Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7W1 |
#6: Protein | Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P02358 |
#7: Protein | Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P02359 |
#8: Protein | Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7W7 |
#9: Protein | Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7X3 |
#10: Protein | Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7R5 |
#11: Protein | Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7R9 |
#12: Protein | Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7S3 |
#13: Protein | Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7S9 |
#14: Protein | Mass: 11677.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0AG59 |
#15: Protein | Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0ADZ4 |
#16: Protein | Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7T3 |
#17: Protein | Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0AG63 |
#18: Protein | Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7T7 |
#19: Protein | Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7U3 |
#20: Protein | Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7U7 |
#21: Protein | Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P68679 |
-Protein , 1 types, 1 molecules z
#25: Protein | Mass: 43239.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0CE48 |
---|
+50S ribosomal protein ... , 31 types, 31 molecules CDEFGHIJKLMNOPQRSTUVWXYZ0123456
-Non-polymers , 8 types, 363 molecules
#59: Chemical | ChemComp-MG / #60: Chemical | #61: Chemical | ChemComp-FME / | #62: Chemical | ChemComp-KIR / | #63: Chemical | ChemComp-GDP / | #64: Chemical | #65: Chemical | #66: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: E. COLI 70S-EF-TU-GDP- KIRROMYCIN-PHE-TRNAPHE- FMET-TRNAFMET-TRNAFMET COMPLEX Type: RIBOSOME |
---|---|
Buffer solution | Name: 50MM HEPES-KOH, 70MMNH4CL, 30MM KCL, 20MM MGCL2, 1MM DTT, 0.6MM SPERMINE, 0.4MM SPERMIDINE, 0.15MM KIRROMYCIN pH: 7.5 Details: 50MM HEPES-KOH, 70MMNH4CL, 30MM KCL, 20MM MGCL2, 1MM DTT, 0.6MM SPERMINE, 0.4MM SPERMIDINE, 0.15MM KIRROMYCIN |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUIDE ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS / Date: Dec 20, 2011 |
Electron gun | Electron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 192000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm / Cs: 0.01 mm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k) |
-Processing
EM software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: LOCAL CTF CORRECTION | ||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Num. of particles: 417201 / Actual pixel size: 0.75525 Å Magnification calibration: CROSS- -CORRELATION WITH PUBLISHED ATOMIC COORDINATES Symmetry type: POINT | ||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||
Refinement | Highest resolution: 2.9 Å |