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Yorodumi- PDB-6s0x: Erythromycin Resistant Staphylococcus aureus 70S ribosome (delta ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s0x | |||||||||
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Title | Erythromycin Resistant Staphylococcus aureus 70S ribosome (delta R88 A89 uL22) in complex with erythromycin. | |||||||||
Components |
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Keywords | RIBOSOME / antibiotics / resistance / Staphylococcus aureus / exit tunnel / RNA / rProteins / erythromycin | |||||||||
Function / homology | Function and homology information large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit ...large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.425 Å | |||||||||
Authors | Halfon, Y. / Matozv, D. / Eyal, Z. / Bashan, A. / Zimmerman, E. / Kjeldgaard, J. / Ingmer, H. / Yonath, A. | |||||||||
Funding support | Denmark, 2items
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Citation | Journal: Sci Rep / Year: 2019 Title: Exit tunnel modulation as resistance mechanism of S. aureus erythromycin resistant mutant. Authors: Yehuda Halfon / Donna Matzov / Zohar Eyal / Anat Bashan / Ella Zimmerman / Jette Kjeldgaard / Hanne Ingmer / Ada Yonath / Abstract: The clinical use of the antibiotic erythromycin (ery) is hampered owing to the spread of resistance genes that are mostly mutating rRNA around the ery binding site at the entrance to the protein exit ...The clinical use of the antibiotic erythromycin (ery) is hampered owing to the spread of resistance genes that are mostly mutating rRNA around the ery binding site at the entrance to the protein exit tunnel. Additional effective resistance mechanisms include deletion or insertion mutations in ribosomal protein uL22, which lead to alterations of the exit tunnel shape, located 16 Å away from the drug's binding site. We determined the cryo-EM structures of the Staphylococcus aureus 70S ribosome, and its ery bound complex with a two amino acid deletion mutation in its ß hairpin loop, which grants the bacteria resistance to ery. The structures reveal that, although the binding of ery is stable, the movement of the flexible shorter uL22 loop towards the tunnel wall creates a wider path for nascent proteins, thus enabling bypass of the barrier formed by the drug. Moreover, upon drug binding, the tunnel widens further. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6s0x.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6s0x.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6s0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s0x_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6s0x_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 6s0x_validation.xml.gz | 359.1 KB | Display | |
Data in CIF | 6s0x_validation.cif.gz | 551.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s0/6s0x ftp://data.pdbj.org/pub/pdb/validation_reports/s0/6s0x | HTTPS FTP |
-Related structure data
Related structure data | 10076MC 6s0zC 6s12C 6s13C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 3 molecules ABa
#1: RNA chain | Mass: 940976.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) |
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#2: RNA chain | Mass: 36974.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1434110260 |
#31: RNA chain | Mass: 498060.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1248686583 |
+50S ribosomal protein ... , 28 types, 28 molecules CDEFGHIJKLMNOPQRSTUVWXYZ1234
-30S ribosomal protein ... , 20 types, 20 molecules bcdefghijklmnopqrstu
#32: Protein | Mass: 25929.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A2X2M020 |
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#33: Protein | Mass: 22684.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UU26 |
#34: Protein | Mass: 22849.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TVK2 |
#35: Protein | Mass: 16522.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TUC9 |
#36: Protein | Mass: 11239.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TPC6 |
#37: Protein | Mass: 17181.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077VHU6 |
#38: Protein | Mass: 14723.118 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U8T8 |
#39: Protein | Mass: 14312.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A1Q4GY48 |
#40: Protein | Mass: 11009.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A0H2K0A0 |
#41: Protein | Mass: 12047.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UKD6 |
#42: Protein | Mass: 15075.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A133PZQ5 |
#43: Protein | Mass: 11991.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U8U6 |
#44: Protein | Mass: 7186.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UGW7 |
#45: Protein | Mass: 10503.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U6H8 |
#46: Protein | Mass: 9993.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U6K4 |
#47: Protein | Mass: 9366.860 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077VLD5 |
#48: Protein | Mass: 6404.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UZF4 |
#49: Protein | Mass: 9205.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A133PYC3 |
#50: Protein | Mass: 8779.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8UXC3 |
#51: Protein | Mass: 6241.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A380DEA2, UniProt: A0A166P928*PLUS |
-Protein / Non-polymers , 2 types, 2 molecules v
#52: Protein | Mass: 18955.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8USK0, UniProt: D2Z097*PLUS |
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#53: Chemical | ChemComp-ERY / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Erythromycin Resistant Staphylococcus aureus 70S ribosome (delta R88 A89 uL22) in complex with erythromycin. Type: RIBOSOME / Entity ID: #1-#52 / Source: NATURAL |
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Source (natural) | Organism: Staphylococcus aureus (bacteria) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.076 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software | Name: RELION / Version: 3 / Category: 3D reconstruction |
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CTF correction | Type: NONE |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 2.425 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 378309 / Symmetry type: POINT |