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Yorodumi- EMDB-30598: Cryo-EM structure of 70S ribosome in complex with peptide deformy... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30598 | ||||||||||||
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Title | Cryo-EM structure of 70S ribosome in complex with peptide deformylase and trigger factor | ||||||||||||
Map data | Cryo-EM density map of E. coli 70S ribosome in complex with peptide deformylase and trigger factor | ||||||||||||
Sample |
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Function / homology | Function and homology information 'de novo' cotranslational protein folding / co-translational protein modification / stress response to copper ion / peptide deformylase / peptide deformylase activity / negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding ...'de novo' cotranslational protein folding / co-translational protein modification / stress response to copper ion / peptide deformylase / peptide deformylase activity / negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / protein unfolding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / translational termination / DnaA-L2 complex / chaperone-mediated protein folding / translation repressor activity / negative regulation of translational initiation / protein folding chaperone / 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 / peptidylprolyl isomerase / ribosomal large subunit assembly / transcription antitermination / peptidyl-prolyl cis-trans isomerase activity / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / ferrous iron binding / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / protein transport / 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 / response to heat / 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 / hydrolase activity / translation / cell division / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
Authors | Akbar S / Bhakta S / Sengupta J | ||||||||||||
Funding support | India, 3 items
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Citation | Journal: Structure / Year: 2021 Title: Structural insights into the interplay of protein biogenesis factors with the 70S ribosome. Authors: Shirin Akbar / Sayan Bhakta / Jayati Sengupta / Abstract: Bacterial co-translational N-terminal methionine excision, an early event of nascent polypeptide chain processing, is mediated by two enzymes: peptide deformylase (PDF) and methionine aminopeptidase ...Bacterial co-translational N-terminal methionine excision, an early event of nascent polypeptide chain processing, is mediated by two enzymes: peptide deformylase (PDF) and methionine aminopeptidase (MetAP). Trigger factor (TF), the only ribosome-associated bacterial chaperone, offers co-translational chaperoning assistance. Here, we present two high-resolution cryoelectron microscopy structures of tRNA-bound E. coli ribosome complexes showing simultaneous binding of PDF and TF, in the absence (3.4 Å) and presence of MetAP (4.1 Å). These structures establish molecular details of the interactions of the factors with the ribosome, and thereby reveal the structural basis of nascent chain processing. Our results suggest that simultaneous binding of all three factors is not a functionally favorable mechanism of nascent chain processing. Strikingly, an unusual structural distortion of the 70S ribosome, potentially driven by binding of multiple copies of MetAP, is observed when MetAP is incubated with a pre-formed PDF-TF-bound ribosome complex. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30598.map.gz | 111.5 MB | EMDB map data format | |
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Header (meta data) | emd-30598-v30.xml emd-30598.xml | 66.5 KB 66.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30598_fsc.xml | 14.5 KB | Display | FSC data file |
Images | emd_30598.png | 191.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30598 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30598 | HTTPS FTP |
-Validation report
Summary document | emd_30598_validation.pdf.gz | 520.2 KB | Display | EMDB validaton report |
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Full document | emd_30598_full_validation.pdf.gz | 519.8 KB | Display | |
Data in XML | emd_30598_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | emd_30598_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30598 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30598 | HTTPS FTP |
-Related structure data
Related structure data | 7d6zMC 7d80C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30598.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM density map of E. coli 70S ribosome in complex with peptide deformylase and trigger factor | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : E. coli 70S ribosome in complex with enzyme peptide deformylase a...
+Supramolecule #1: E. coli 70S ribosome in complex with enzyme peptide deformylase a...
+Macromolecule #1: 30S ribosomal protein S20
+Macromolecule #2: 30S ribosomal protein S21
+Macromolecule #6: 50S ribosomal protein L31
+Macromolecule #9: 50S ribosomal protein L2
+Macromolecule #10: 50S ribosomal protein L3
+Macromolecule #11: 50S ribosomal protein L4
+Macromolecule #12: 50S ribosomal protein L5
+Macromolecule #13: 50S ribosomal protein L6
+Macromolecule #14: 50S ribosomal protein L9
+Macromolecule #15: 50S ribosomal protein L11
+Macromolecule #16: 50S ribosomal protein L13
+Macromolecule #17: 50S ribosomal protein L14
+Macromolecule #18: 50S ribosomal protein L15
+Macromolecule #19: 50S ribosomal protein L16
+Macromolecule #20: 50S ribosomal protein L17
+Macromolecule #21: 50S ribosomal protein L18
+Macromolecule #22: 50S ribosomal protein L19
+Macromolecule #23: 50S ribosomal protein L20
+Macromolecule #24: 50S ribosomal protein L21
+Macromolecule #25: 50S ribosomal protein L22
+Macromolecule #26: 50S ribosomal protein L30
+Macromolecule #27: 50S ribosomal protein L24
+Macromolecule #28: 50S ribosomal protein L25
+Macromolecule #29: 50S ribosomal protein L27
+Macromolecule #30: 50S ribosomal protein L28
+Macromolecule #31: 50S ribosomal protein L29
+Macromolecule #32: 50S ribosomal protein L23
+Macromolecule #33: 50S ribosomal protein L32
+Macromolecule #34: 50S ribosomal protein L33
+Macromolecule #35: 50S ribosomal protein L34
+Macromolecule #36: 50S ribosomal protein L35
+Macromolecule #37: 50S ribosomal protein L36
+Macromolecule #39: Peptide deformylase
+Macromolecule #40: Trigger factor
+Macromolecule #41: 30S ribosomal protein S2
+Macromolecule #42: 30S ribosomal protein S3
+Macromolecule #43: 30S ribosomal protein S4
+Macromolecule #44: 30S ribosomal protein S5
+Macromolecule #45: 30S ribosomal protein S6, fully modified isoform
+Macromolecule #46: 30S ribosomal protein S7
+Macromolecule #47: 30S ribosomal protein S8
+Macromolecule #48: 30S ribosomal protein S9
+Macromolecule #49: 30S ribosomal protein S10
+Macromolecule #50: 30S ribosomal protein S11
+Macromolecule #51: 30S ribosomal protein S12
+Macromolecule #52: 30S ribosomal protein S13
+Macromolecule #53: 30S ribosomal protein S14
+Macromolecule #54: 30S ribosomal protein S15
+Macromolecule #55: 30S ribosomal protein S16
+Macromolecule #56: 30S ribosomal protein S17
+Macromolecule #57: 30S ribosomal protein S18
+Macromolecule #58: 30S ribosomal protein S19
+Macromolecule #3: E-site tRNA
+Macromolecule #4: P-site tRNA
+Macromolecule #5: A-site tRNA
+Macromolecule #7: 23S ribosomal rRNA
+Macromolecule #8: 5S ribosomal rRNA
+Macromolecule #38: 16S ribosomal rRNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 32.57 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |