[English] 日本語
Yorodumi- PDB-8am9: Cryo-EM structure of the proline-rich antimicrobial peptide droso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8am9 | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the elongating ribosome | ||||||
Components |
| ||||||
Keywords | RIBOSOME / E.coli / 70S / Drosocin / Dro1 / antimicrobial peptide / proline-rich / PrAMP / Initiator tRNA / Elongation / Leucine tRNA | ||||||
Function / homology | Function and homology information ornithine decarboxylase inhibitor activity / four-way junction DNA binding / DNA endonuclease activity / ribosomal large subunit assembly / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit ...ornithine decarboxylase inhibitor activity / four-way junction DNA binding / DNA endonuclease activity / ribosomal large subunit assembly / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / 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 / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) Escherichia coli BW25113 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Koller, T.O. / Morici, M. / Wilson, D.N. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Nat Chem Biol / Year: 2023 Title: Structural basis for translation inhibition by the glycosylated drosocin peptide. Authors: Timm O Koller / Martino Morici / Max Berger / Haaris A Safdari / Deepti S Lele / Bertrand Beckert / Kanwal J Kaur / Daniel N Wilson / Abstract: The proline-rich antimicrobial peptide (PrAMP) drosocin is produced by Drosophila species to combat bacterial infection. Unlike many PrAMPs, drosocin is O-glycosylated at threonine 11, a post- ...The proline-rich antimicrobial peptide (PrAMP) drosocin is produced by Drosophila species to combat bacterial infection. Unlike many PrAMPs, drosocin is O-glycosylated at threonine 11, a post-translation modification that enhances its antimicrobial activity. Here we demonstrate that the O-glycosylation not only influences cellular uptake of the peptide but also interacts with its intracellular target, the ribosome. Cryogenic electron microscopy structures of glycosylated drosocin on the ribosome at 2.0-2.8-Å resolution reveal that the peptide interferes with translation termination by binding within the polypeptide exit tunnel and trapping RF1 on the ribosome, reminiscent of that reported for the PrAMP apidaecin. The glycosylation of drosocin enables multiple interactions with U2609 of the 23S rRNA, leading to conformational changes that break the canonical base pair with A752. Collectively, our study reveals novel molecular insights into the interaction of O-glycosylated drosocin with the ribosome, which provide a structural basis for future development of this class of antimicrobials. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8am9.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8am9.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8am9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8am9_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8am9_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8am9_validation.xml.gz | 217.4 KB | Display | |
Data in CIF | 8am9_validation.cif.gz | 377.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/8am9 ftp://data.pdbj.org/pub/pdb/validation_reports/am/8am9 | HTTPS FTP |
-Related structure data
Related structure data | 15523MC 8aknC 8anaC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
+50S ribosomal protein ... , 29 types, 29 molecules 01234cdefghijklmnopqrstuvwxyz
-RNA chain , 6 types, 6 molecules BabXY8
#6: RNA chain | Mass: 497404.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) |
---|---|
#27: RNA chain | Mass: 941477.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) |
#28: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) |
#53: RNA chain | Mass: 3815.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) |
#54: RNA chain | Mass: 24541.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) |
#55: RNA chain | Mass: 27424.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) |
-30S ribosomal protein ... , 20 types, 20 molecules CDEFGHIJKLMNOPQRSTUV
#7: Protein | Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7V0 |
---|---|
#8: Protein | Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A3S7D3V3 |
#9: Protein | Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: C3SR62 |
#10: Protein | Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A5V7D7L3 |
#11: Protein | Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02358 |
#12: Protein | Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02359 |
#13: Protein | Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A829CDV3 |
#14: Protein | Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A8E2LXD9 |
#15: Protein | Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A836N8P1 |
#16: Protein | Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A7U9G2M1 |
#17: Protein | Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A0K0HEP7 |
#18: Protein | Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: C3SR52 |
#19: Protein | Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A2S8DCV7 |
#20: Protein | Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: C3SSQ7 |
#21: Protein | Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7T3 |
#22: Protein | Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: E3GBX2 |
#23: Protein | Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A7L6DXG2 |
#24: Protein | Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A829ADD3 |
#25: Protein | Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7U7 |
#26: Protein | Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: E9TH65 |
-Protein/peptide / Sugars , 2 types, 2 molecules A
#56: Protein/peptide | Type: Peptide-like / Class: Antimicrobial / Mass: 2204.579 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dwil\GK19342, Dwil_GK19342 / Production host: Escherichia coli BW25113 (bacteria) / References: UniProt: B4MNS1, BIRD: PRD_002425 |
---|---|
#60: Sugar | ChemComp-A2G / |
-Non-polymers , 4 types, 298 molecules
#57: Chemical | #58: Chemical | ChemComp-MG / #59: Chemical | ChemComp-SPM / | #61: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the elongating ribosome Type: RIBOSOME / Entity ID: #1-#3, #7-#26, #31-#51, #53-#55 / Source: NATURAL | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 2.2 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Escherichia coli K-12 (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 8 OD260/mL | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R3/3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 278 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 900 nm / Nominal defocus min: 400 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
EM software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84697 / Symmetry type: POINT | |||||||||||||||||||||||||
Refine LS restraints |
|