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Yorodumi- EMDB-0243: Improved model derived from cryo-EM map of Staphylococcus aureus ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0243 | |||||||||
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Title | Improved model derived from cryo-EM map of Staphylococcus aureus large ribosomal subunit | |||||||||
Map data | resolution 2.65 A | |||||||||
Sample |
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Function / homology | Function and homology information ribosomal large subunit assembly / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation ...ribosomal large subunit assembly / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.65 Å | |||||||||
Authors | Eyal Z / Cimicata G / Matzov D / Fox T / de Val N / Zimmerman E / Bashan A / Yonath A | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2015 Title: Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus. Authors: Zohar Eyal / Donna Matzov / Miri Krupkin / Itai Wekselman / Susanne Paukner / Ella Zimmerman / Haim Rozenberg / Anat Bashan / Ada Yonath / Abstract: The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from ...The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus. | |||||||||
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_0243.map.gz | 126.2 MB | EMDB map data format | |
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Header (meta data) | emd-0243-v30.xml emd-0243.xml | 43 KB 43 KB | Display Display | EMDB header |
Images | emd_0243.png | 164.4 KB | ||
Others | emd_0243_additional.map.gz emd_0243_half_map_1.map.gz emd_0243_half_map_2.map.gz | 105.9 MB 106.1 MB 106.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0243 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0243 | HTTPS FTP |
-Validation report
Summary document | emd_0243_validation.pdf.gz | 489.9 KB | Display | EMDB validaton report |
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Full document | emd_0243_full_validation.pdf.gz | 489.1 KB | Display | |
Data in XML | emd_0243_validation.xml.gz | 12.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0243 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0243 | HTTPS FTP |
-Related structure data
Related structure data | 6hmaMC M: atomic model generated by this map C: citing same article (ref.) |
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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_0243.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | resolution 2.65 A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.858 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: resolution 2.87 A
File | emd_0243_additional.map | ||||||||||||
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Annotation | resolution 2.87 A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_0243_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_0243_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Staphylococcus aureus large ribosomal subunit
+Supramolecule #1: Staphylococcus aureus large ribosomal subunit
+Macromolecule #1: 23S ribosomal RNA
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #3: 50S ribosomal protein L2
+Macromolecule #4: 50S ribosomal protein L3
+Macromolecule #5: 50S ribosomal protein L4
+Macromolecule #6: 50S ribosomal protein L5
+Macromolecule #7: 50S ribosomal protein L6
+Macromolecule #8: 50S ribosomal protein L13
+Macromolecule #9: 50S ribosomal protein L14
+Macromolecule #10: 50S ribosomal protein L15
+Macromolecule #11: 50S ribosomal protein L16
+Macromolecule #12: 50S ribosomal protein L17
+Macromolecule #13: 50S ribosomal protein L18
+Macromolecule #14: 50S ribosomal protein L19
+Macromolecule #15: 50S ribosomal protein L20
+Macromolecule #16: 50S ribosomal protein L21
+Macromolecule #17: 50S ribosomal protein L22
+Macromolecule #18: 50S ribosomal protein L23
+Macromolecule #19: 50S ribosomal protein L24
+Macromolecule #20: 50S ribosomal protein L25
+Macromolecule #21: 50S ribosomal protein L27
+Macromolecule #22: 50S ribosomal protein L28
+Macromolecule #23: 50S ribosomal protein L29
+Macromolecule #24: 50S ribosomal protein L30
+Macromolecule #25: 50S ribosomal protein L32
+Macromolecule #26: 50S ribosomal protein L33
+Macromolecule #27: 50S ribosomal protein L34
+Macromolecule #28: 50S ribosomal protein L35
+Macromolecule #29: 50S ribosomal protein L36
+Macromolecule #30: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.6 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 211046 |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |