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Yorodumi- EMDB-9753: Cryo-EM density map of peptide deformylase and methionine aminope... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9753 | |||||||||
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Title | Cryo-EM density map of peptide deformylase and methionine aminopeptidase bound to the E. coli 70S ribosome | |||||||||
Map data | E.coli Peptide deformylsae and Methionine aminopeptidase bound to E.coli 70S ribosome at the polypeptide exit tunnel. | |||||||||
Sample |
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Keywords | E. coli 70S ribosome / Protein biogenesis / Peptide deformylase / Methionine aminopeptidase / Polypeptide exit tunnel / RIBOSOME | |||||||||
Function / homology | Function and homology information co-translational protein modification / peptide deformylase / peptide deformylase activity / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / ferrous iron binding / ribosome binding / hydrolase activity / translation ...co-translational protein modification / peptide deformylase / peptide deformylase activity / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / ferrous iron binding / ribosome binding / hydrolase activity / translation / proteolysis / zinc ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.8 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_9753.map.gz | 38.3 MB | EMDB map data format | |
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Header (meta data) | emd-9753-v30.xml emd-9753.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9753_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_9753.png | 152.3 KB | ||
Filedesc metadata | emd-9753.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9753 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9753 | HTTPS FTP |
-Validation report
Summary document | emd_9753_validation.pdf.gz | 492.1 KB | Display | EMDB validaton report |
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Full document | emd_9753_full_validation.pdf.gz | 491.6 KB | Display | |
Data in XML | emd_9753_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_9753_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9753 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9753 | HTTPS FTP |
-Related structure data
Related structure data | 6iziMC 9750C 9752C 9759C 9778C 6iy7C 6iz7C 6j0aC 6j45C 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_9753.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | E.coli Peptide deformylsae and Methionine aminopeptidase bound to E.coli 70S ribosome at the polypeptide exit tunnel. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 peptide deformylase and meth...
Entire | Name: E. coli 70S ribosome in complex with peptide deformylase and methionine aminopeptidase |
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Components |
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-Supramolecule #1: E. coli 70S ribosome in complex with peptide deformylase and meth...
Supramolecule | Name: E. coli 70S ribosome in complex with peptide deformylase and methionine aminopeptidase type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli K-12 (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 K-12 (bacteria) / Strain: K-12 |
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: Methionine aminopeptidase
Macromolecule | Name: Methionine aminopeptidase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: methionyl aminopeptidase |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K-12 |
Molecular weight | Theoretical: 29.341775 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAISIKTPED IEKMRVAGRL AAEVLEMIEP YVKPGVSTGE LDRICNDYIV NEQHAVSACL GYHGYPKSVC ISINEVVCHG IPDDAKLLK DGDIVNIDVT VIKDGFHGDT SKMFIVGKPT IMGERLCRIT QESLYLALRM VKPGINLREI GAAIQKFVEA E GFSVVREY ...String: MAISIKTPED IEKMRVAGRL AAEVLEMIEP YVKPGVSTGE LDRICNDYIV NEQHAVSACL GYHGYPKSVC ISINEVVCHG IPDDAKLLK DGDIVNIDVT VIKDGFHGDT SKMFIVGKPT IMGERLCRIT QESLYLALRM VKPGINLREI GAAIQKFVEA E GFSVVREY CGHGIGQGFH EEPQVLHYDS RETNVVLKPG MTFTIEPMVN AGKKEIRTMK DGWTVKTKDR SLSAQYEHTI VV TDNGCEI LTLRKDDTIP AIISHDE UniProtKB: Methionine aminopeptidase |
-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-6izi: |