+Open data
-Basic information
Entry | Database: PDB / ID: 5zlu | ||||||
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Title | Ribosome Structure bound to ABC-F protein. | ||||||
Components |
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Keywords | RIBOSOME / Antibiotics / Macrolides / ABC-F protein / AZM | ||||||
Function / homology | Function and homology information endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding ...endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / large ribosomal subunit / 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 / 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 / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) Thermus thermophilus (bacteria) Thermus thermophilus HB8 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Su, W.X. / Kumar, V. / Ero, R. / Andrew, S.W.W. / Jian, S. / Yong-Gui, G. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2018 Title: Ribosome protection by antibiotic resistance ATP-binding cassette protein. Authors: Weixin Su / Veerendra Kumar / Yichen Ding / Rya Ero / Aida Serra / Benjamin Sian Teck Lee / Andrew See Weng Wong / Jian Shi / Siu Kwan Sze / Liang Yang / Yong-Gui Gao / Abstract: The ribosome is one of the richest targets for antibiotics. Unfortunately, antibiotic resistance is an urgent issue in clinical practice. Several ATP-binding cassette family proteins confer ...The ribosome is one of the richest targets for antibiotics. Unfortunately, antibiotic resistance is an urgent issue in clinical practice. Several ATP-binding cassette family proteins confer resistance to ribosome-targeting antibiotics through a yet unknown mechanism. Among them, MsrE has been implicated in macrolide resistance. Here, we report the cryo-EM structure of ATP form MsrE bound to the ribosome. Unlike previously characterized ribosomal protection proteins, MsrE is shown to bind to ribosomal exit site. Our structure reveals that the domain linker forms a unique needle-like arrangement with two crossed helices connected by an extended loop projecting into the peptidyl-transferase center and the nascent peptide exit tunnel, where numerous antibiotics bind. In combination with biochemical assays, our structure provides insight into how MsrE binding leads to conformational changes, which results in the release of the drug. This mechanism appears to be universal for the ABC-F type ribosome protection proteins. | ||||||
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 | 5zlu.cif.gz | 3.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5zlu.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5zlu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zlu_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5zlu_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5zlu_validation.xml.gz | 235.9 KB | Display | |
Data in CIF | 5zlu_validation.cif.gz | 409.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/5zlu ftp://data.pdbj.org/pub/pdb/validation_reports/zl/5zlu | HTTPS FTP |
-Related structure data
Related structure data | 6934MC 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 , 5 types, 5 molecules WGVXDD
#1: RNA chain | Mass: 8156.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus HB8 (bacteria) |
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#8: RNA chain | Mass: 491471.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 |
#23: RNA chain | Mass: 935028.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 |
#24: RNA chain | Mass: 39846.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: GenBank: 37223181 |
#55: RNA chain | Mass: 24885.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus HB8 (bacteria) |
-30S ribosomal protein ... , 20 types, 20 molecules ABCDEFHIJKLMNOPQRSTU
#2: Protein | Mass: 12193.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P24321 |
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#3: Protein | Mass: 8483.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80382 |
#4: Protein | Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380 |
#5: Protein | Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2 |
#6: Protein | Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7 |
#7: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3 |
#9: Protein | Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371 |
#10: Protein | Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372 |
#11: Protein | Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80373 |
#12: Protein | Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5 |
#13: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8 |
#14: Protein | Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P17291 |
#15: Protein | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY9 |
#16: Protein | Mass: 14410.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374 |
#17: Protein | Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376 |
#18: Protein | Mass: 14637.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3 |
#19: Protein | Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377 |
#20: Protein | Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY6 |
#21: Protein | Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76 |
#22: Protein | Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3 |
+50S ribosomal protein ... , 30 types, 31 molecules YZabcdefghijklmnopqrstuvwCCxyzAABB
-Protein , 1 types, 1 molecules EE
#56: Protein | Mass: 55706.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: mel / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I9WCL8 |
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-Non-polymers , 2 types, 4 molecules
#57: Chemical | #58: Chemical | |
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-Details
Sequence details | Natural variant at this position |
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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: Bacterial ribosome in complex with MsrE / Type: RIBOSOME / Entity ID: #1-#55 / Source: MULTIPLE SOURCES | ||||||||||||||||||||
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Molecular weight | Value: 2.8 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Thermus thermophilus (bacteria) / Strain: HB8 | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||
EM embedding | Material: Ice | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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 / Cs: 2.7 mm |
Image recording | Electron dose: 50 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127778 / Num. of class averages: 15 / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||
Refinement | Highest resolution: 3.6 Å |