+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20638 | |||||||||
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Title | E. coli 50S with phazolicin (PHZ) bound in exit tunnel | |||||||||
Map data | Charge density map used for real space refine, obtained as described by Wang, J. (2017) | |||||||||
Sample |
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Keywords | ribosome / phazolicin / antimicrobial protein / RIBOSOME-INHIBITOR complex | |||||||||
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 / tRNA binding / cytoplasmic translation / rRNA binding / ribosome ...ribosomal large subunit assembly / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Rhizobium sp. Pop5 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.87 Å | |||||||||
Authors | Watson ZL / Cate JHD | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition. Authors: Dmitrii Y Travin / Zoe L Watson / Mikhail Metelev / Fred R Ward / Ilya A Osterman / Irina M Khven / Nelli F Khabibullina / Marina Serebryakova / Peter Mergaert / Yury S Polikanov / Jamie H D ...Authors: Dmitrii Y Travin / Zoe L Watson / Mikhail Metelev / Fred R Ward / Ilya A Osterman / Irina M Khven / Nelli F Khabibullina / Marina Serebryakova / Peter Mergaert / Yury S Polikanov / Jamie H D Cate / Konstantin Severinov / Abstract: Ribosome-synthesized post-translationally modified peptides (RiPPs) represent a rapidly expanding class of natural products with various biological activities. Linear azol(in)e-containing peptides ...Ribosome-synthesized post-translationally modified peptides (RiPPs) represent a rapidly expanding class of natural products with various biological activities. Linear azol(in)e-containing peptides (LAPs) comprise a subclass of RiPPs that display outstanding diversity of mechanisms of action while sharing common structural features. Here, we report the discovery of a new LAP biosynthetic gene cluster in the genome of Rhizobium Pop5, which encodes the precursor peptide and modification machinery of phazolicin (PHZ) - an extensively modified peptide exhibiting narrow-spectrum antibacterial activity against some symbiotic bacteria of leguminous plants. The cryo-EM structure of the Escherichia coli 70S-PHZ complex reveals that the drug interacts with the 23S rRNA and uL4/uL22 proteins and obstructs ribosomal exit tunnel in a way that is distinct from other compounds. We show that the uL4 loop sequence determines the species-specificity of antibiotic action. PHZ expands the known diversity of LAPs and may be used in the future as biocontrol agent for agricultural needs. | |||||||||
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_20638.map.gz | 84 MB | EMDB map data format | |
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Header (meta data) | emd-20638-v30.xml emd-20638.xml | 56.1 KB 56.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20638_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_20638.png | 155.7 KB | ||
Masks | emd_20638_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-20638.cif.gz | 11.1 KB | ||
Others | emd_20638_additional_1.map.gz emd_20638_additional_2.map.gz emd_20638_half_map_1.map.gz emd_20638_half_map_2.map.gz | 116.7 MB 98.1 MB 98.4 MB 98.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20638 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20638 | HTTPS FTP |
-Validation report
Summary document | emd_20638_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_20638_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_20638_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | emd_20638_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20638 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20638 | HTTPS FTP |
-Related structure data
Related structure data | 6u48MC 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_20638.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Charge density map used for real space refine, obtained as described by Wang, J. (2017) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1136 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_20638_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: RELION post-processed map, used for preview image
File | emd_20638_additional_1.map | ||||||||||||
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Annotation | RELION post-processed map, used for preview image | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: RELION 3D auto-refine map
File | emd_20638_additional_2.map | ||||||||||||
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Annotation | RELION 3D auto-refine map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map #1
File | emd_20638_half_map_1.map | ||||||||||||
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Annotation | half map #1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map #2
File | emd_20638_half_map_2.map | ||||||||||||
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Annotation | half map #2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : E. coli ribosome with phazolicin in exit tunnel
+Supramolecule #1: E. coli ribosome with phazolicin in exit tunnel
+Supramolecule #2: E. coli 50S
+Supramolecule #3: Phazolicin
+Macromolecule #1: 23S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #3: 50S ribosomal protein uL2
+Macromolecule #4: 50S ribosomal protein uL3
+Macromolecule #5: 50S ribosomal protein uL4
+Macromolecule #6: 50S ribosomal protein uL5
+Macromolecule #7: 50S ribosomal protein uL6
+Macromolecule #8: 50S ribosomal protein bL9
+Macromolecule #9: 50S ribosomal protein uL11
+Macromolecule #10: 50S ribosomal protein uL13
+Macromolecule #11: 50S ribosomal protein uL14
+Macromolecule #12: 50S ribosomal protein uL15
+Macromolecule #13: 50S ribosomal protein uL16
+Macromolecule #14: 50S ribosomal protein bL17
+Macromolecule #15: 50S ribosomal protein uL18
+Macromolecule #16: 50S ribosomal protein bL19
+Macromolecule #17: 50S ribosomal protein bL20
+Macromolecule #18: 50S ribosomal protein bL21
+Macromolecule #19: 50S ribosomal protein uL22
+Macromolecule #20: 50S ribosomal protein uL23
+Macromolecule #21: 50S ribosomal protein uL24
+Macromolecule #22: 50S ribosomal protein bL25
+Macromolecule #23: 50S ribosomal protein bL27
+Macromolecule #24: 50S ribosomal protein bL28
+Macromolecule #25: 50S ribosomal protein uL29
+Macromolecule #26: 50S ribosomal protein uL30
+Macromolecule #27: 50S ribosomal protein bL32
+Macromolecule #28: 50S ribosomal protein bL33
+Macromolecule #29: 50S ribosomal protein bL34
+Macromolecule #30: 50S ribosomal protein bL35
+Macromolecule #31: 50S ribosomal protein bL36
+Macromolecule #32: phazolicin
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Details: unspecified |
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: 30.0 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 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |