+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6934 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Ribosome Structure bound to ABC-F protein. | |||||||||
Map data | None | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information 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 ...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 / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) / Thermus thermophilus HB8 (bacteria) / Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) / Pseudomonas aeruginosa (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Su WX / Kumar V / Ero R / Andrew SWW / Jian S / Yong-Gui G | |||||||||
Funding support | Singapore, 1 items
| |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6934.map.gz | 25 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6934-v30.xml emd-6934.xml | 70.4 KB 70.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6934_fsc.xml | 12.5 KB | Display | FSC data file |
Images | emd_6934.png | 253.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6934 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6934 | HTTPS FTP |
-Validation report
Summary document | emd_6934_validation.pdf.gz | 434.9 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_6934_full_validation.pdf.gz | 434.5 KB | Display | |
Data in XML | emd_6934_validation.xml.gz | 13 KB | Display | |
Data in CIF | emd_6934_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6934 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6934 | HTTPS FTP |
-Related structure data
Related structure data | 5zluMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_6934.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : Bacterial ribosome in complex with MsrE
+Supramolecule #1: Bacterial ribosome in complex with MsrE
+Macromolecule #1: RNA (25-mer)
+Macromolecule #8: 16S ribosomal RNA
+Macromolecule #23: 23S ribosomal RNA
+Macromolecule #24: 5S ribosomal RNA
+Macromolecule #55: P-site tRNA
+Macromolecule #2: 30S ribosomal protein S17
+Macromolecule #3: 30S ribosomal protein S18
+Macromolecule #4: 30S ribosomal protein S20
+Macromolecule #5: 30S ribosomal protein S19
+Macromolecule #6: 30S ribosomal protein S10
+Macromolecule #7: 30S ribosomal protein Thx
+Macromolecule #9: 30S ribosomal protein S2
+Macromolecule #10: 30S ribosomal protein S3
+Macromolecule #11: 30S ribosomal protein S4
+Macromolecule #12: 30S ribosomal protein S5
+Macromolecule #13: 30S ribosomal protein S6
+Macromolecule #14: 30S ribosomal protein S7
+Macromolecule #15: 30S ribosomal protein S8
+Macromolecule #16: 30S ribosomal protein S9
+Macromolecule #17: 30S ribosomal protein S11
+Macromolecule #18: 30S ribosomal protein S12
+Macromolecule #19: 30S ribosomal protein S13
+Macromolecule #20: 30S ribosomal protein S14 type Z
+Macromolecule #21: 30S ribosomal protein S15
+Macromolecule #22: 30S ribosomal protein S16
+Macromolecule #25: 50S ribosomal protein L1
+Macromolecule #26: 50S ribosomal protein L2
+Macromolecule #27: 50S ribosomal protein L3
+Macromolecule #28: 50S ribosomal protein L4
+Macromolecule #29: 50S ribosomal protein L5
+Macromolecule #30: 50S ribosomal protein L6
+Macromolecule #31: 50S ribosomal protein L10
+Macromolecule #32: 50S ribosomal protein L11
+Macromolecule #33: 50S ribosomal protein L13
+Macromolecule #34: 50S ribosomal protein L14
+Macromolecule #35: 50S ribosomal protein L15
+Macromolecule #36: 50S ribosomal protein L16
+Macromolecule #37: 50S ribosomal protein L17
+Macromolecule #38: 50S ribosomal protein L18
+Macromolecule #39: 50S ribosomal protein L19
+Macromolecule #40: 50S ribosomal protein L20
+Macromolecule #41: 50S ribosomal protein L21
+Macromolecule #42: 50S ribosomal protein L22
+Macromolecule #43: 50S ribosomal protein L23
+Macromolecule #44: 50S ribosomal protein L24
+Macromolecule #45: 50S ribosomal protein L25
+Macromolecule #46: 50S ribosomal protein L27
+Macromolecule #47: 50S ribosomal protein L29
+Macromolecule #48: 50S ribosomal protein L30
+Macromolecule #49: 50S ribosomal protein L31
+Macromolecule #50: 50S ribosomal protein L32
+Macromolecule #51: 50S ribosomal protein L33
+Macromolecule #52: 50S ribosomal protein L34
+Macromolecule #53: 50S ribosomal protein L35
+Macromolecule #54: 50S ribosomal protein L36
+Macromolecule #56: Macrolide efflux protein
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sugar embedding | Material: Ice | ||||||||||||
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 0.2 nm / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
---|---|
Output model | PDB-5zlu: |