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Yorodumi- EMDB-9778: Cryo-EM density map of peptide deformylase enzyme and chaperone t... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9778 | |||||||||
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Title | Cryo-EM density map of peptide deformylase enzyme and chaperone trigger factor bound to the E. coli 70S ribosome | |||||||||
Map data | Cryo EM structure of E. coli 70S ribosome in complex with enzyme peptide deformylase and chaperone trigger factor | |||||||||
Sample |
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Keywords | E. coli 70S ribosome / Protein biogenesis / Chaperone / Peptide deformylase / Trigger factor / Polypeptide exit tunnel / PPIase / RIBOSOME | |||||||||
Function / homology | Function and homology information cell cycle / peptide deformylase / peptide deformylase activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein transport / protein folding / translation / cell division / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli H591 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.2 Å | |||||||||
Authors | Sengupta J / Bhakta S | |||||||||
Funding support | India, 2 items
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Citation | Journal: J Mol Biol / Year: 2019 Title: Cryo-EM Structures Reveal Relocalization of MetAP in the Presence of Other Protein Biogenesis Factors at the Ribosomal Tunnel Exit. Authors: Sayan Bhakta / Shirin Akbar / Jayati Sengupta / Abstract: During protein biosynthesis in bacteria, one of the earliest events that a nascent polypeptide chain goes through is the co-translational enzymatic processing. The event includes two enzymatic ...During protein biosynthesis in bacteria, one of the earliest events that a nascent polypeptide chain goes through is the co-translational enzymatic processing. The event includes two enzymatic pathways: deformylation of the N-terminal methionine by the enzyme peptide deformylase (PDF), followed by methionine excision catalyzed by methionine aminopeptidase (MetAP). During the enzymatic processing, the emerging nascent protein likely remains shielded by the ribosome-associated chaperone trigger factor. The ribosome tunnel exit serves as a stage for recruiting proteins involved in maturation processes of the nascent chain. Co-translational processing of nascent chains is a critical step for subsequent folding and functioning of mature proteins. Here, we present cryo-electron microscopy structures of Escherichia coli (E. coli) ribosome in complex with the nascent chain processing proteins. The structures reveal overlapping binding sites for PDF and MetAP when they bind individually at the tunnel exit site, where L22-L32 protein region provides primary anchoring sites for both proteins. In the absence of PDF, trigger factor can access ribosomal tunnel exit when MetAP occupies its primary binding site. Interestingly, however, in the presence of PDF, when MetAP's primary binding site is already engaged, MetAP has a remarkable ability to occupy an alternative binding site adjacent to PDF. Our study, thus, discloses an unexpected mechanism that MetAP adopts for context-specific ribosome association. | |||||||||
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_9778.map.gz | 38.3 MB | EMDB map data format | |
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Header (meta data) | emd-9778-v30.xml emd-9778.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9778_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_9778.png | 124.7 KB | ||
Filedesc metadata | emd-9778.cif.gz | 6.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9778 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9778 | HTTPS FTP |
-Validation report
Summary document | emd_9778_validation.pdf.gz | 505.5 KB | Display | EMDB validaton report |
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Full document | emd_9778_full_validation.pdf.gz | 505.1 KB | Display | |
Data in XML | emd_9778_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_9778_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9778 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9778 | HTTPS FTP |
-Related structure data
Related structure data | 6j45MC 9750C 9752C 9753C 9759C 6iy7C 6iz7C 6iziC 6j0aC C: citing same article (ref.) M: atomic model generated by this map |
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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_9778.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo EM structure of E. coli 70S ribosome in complex with enzyme peptide deformylase and chaperone trigger factor | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.89 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...
Entire | Name: E. coli 70S ribosome in complex with enzyme peptide deformylase and chaperone trigger factor |
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Components |
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-Supramolecule #1: E. coli 70S ribosome in complex with enzyme peptide deformylase a...
Supramolecule | Name: E. coli 70S ribosome in complex with enzyme peptide deformylase and chaperone trigger factor type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: The complex was prepared by incubating E. coli 70S ribosome with peptide deformylase, methionine aminopeptidase and trigger factor in that sequence. However, cryo EM reconstruction of the ...Details: The complex was prepared by incubating E. coli 70S ribosome with peptide deformylase, methionine aminopeptidase and trigger factor in that sequence. However, cryo EM reconstruction of the complex showed no density corresponding to methionine aminopeptidase near the ribosomal tunnel exit. |
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Source (natural) | Organism: Escherichia coli H591 (bacteria) |
-Macromolecule #1: Peptide deformylase
Macromolecule | Name: Peptide deformylase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptide deformylase |
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Source (natural) | Organism: Escherichia coli H591 (bacteria) |
Molecular weight | Theoretical: 19.357447 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSVLQVLHIP DERLRKVAKP VEEVNAEIQR IVDDMFETMY AEEGIGLAAT QVDIHQRIIV IDVSENRDER LVLINPELLE KSGETGIEE GCLSIPEQRA LVPRAEKVKI RALDRDGKPF ELEADGLLAI CIQHEMDHLV GKLFMDYLSP LKQQRIRQKV E KLDRLKAR A UniProtKB: Peptide deformylase |
-Macromolecule #2: Trigger factor
Macromolecule | Name: Trigger factor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase |
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Source (natural) | Organism: Escherichia coli H591 (bacteria) |
Molecular weight | Theoretical: 48.25557 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MQVSVETTQG LGRRVTITIA ADSIETAVKS ELVNVAKKVR IDGFRKGKVP MNIVAQRYGA SVRQDVLGDL MSRNFIDAII KEKINPAGA PTYVPGEYKL GEDFTYSVEF EVYPEVELQG LEAIEVEKPI VEVTDADVDG MLDTLRKQQA TWKEKDGAVE A EDRVTIDF ...String: MQVSVETTQG LGRRVTITIA ADSIETAVKS ELVNVAKKVR IDGFRKGKVP MNIVAQRYGA SVRQDVLGDL MSRNFIDAII KEKINPAGA PTYVPGEYKL GEDFTYSVEF EVYPEVELQG LEAIEVEKPI VEVTDADVDG MLDTLRKQQA TWKEKDGAVE A EDRVTIDF TGSVDGEEFE GGKASDFVLA MGQGRMIPGF EDGIKGHKAG EEFTIDVTFP EEYHAENLKG KAAKFAINLK KV EERELPE LTAEFIKRFG VEDGSVEGLR AEVRKNMERE LKSAIRNRVK SQAIEGLVKA NDIDVPAALI DSEIDVLRRQ AAQ RFGGNE KQALELPREL FEEQAKRRVV VGLLLGEVIR TNELKADEER VKGLIEEMAS AYEDPKEVIE FYSKNKELMD NMRN VALEE QAVEAVLAKA KVTEKETTFN ELMNQQA UniProtKB: Trigger factor |
-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 R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: FEI EAGLE (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 10.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Output model | PDB-6j45: |