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Yorodumi- EMDB-23588: Cryo-EM map of the elongation module of the bacillamide NRPS, Bmd... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23588 | |||||||||
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Title | Cryo-EM map of the elongation module of the bacillamide NRPS, BmdB, complexed with the oxidase BmdC | |||||||||
Map data | EM Map of the elongation module of the bacillamide NRPS, BmdB, complexed with the oxidase BmdC | |||||||||
Sample |
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Biological species | Thermoactinomyces vulgaris (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Sharon I / Strauss M / Schmeing TM | |||||||||
Funding support | Canada, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structures and function of a tailoring oxidase in complex with a nonribosomal peptide synthetase module. Authors: Camille Marie Fortinez / Kristjan Bloudoff / Connor Harrigan / Itai Sharon / Mike Strauss / T Martin Schmeing / Abstract: Nonribosomal peptide synthetases (NRPSs) are large modular enzymes that synthesize secondary metabolites and natural product therapeutics. Most NRPS biosynthetic pathways include an NRPS and ...Nonribosomal peptide synthetases (NRPSs) are large modular enzymes that synthesize secondary metabolites and natural product therapeutics. Most NRPS biosynthetic pathways include an NRPS and additional proteins that introduce chemical modifications before, during or after assembly-line synthesis. The bacillamide biosynthetic pathway is a common, three-protein system, with a decarboxylase that prepares an NRPS substrate, an NRPS, and an oxidase. Here, the pathway is reconstituted in vitro. The oxidase is shown to perform dehydrogenation of the thiazoline in the peptide intermediate while it is covalently attached to the NRPS, as the penultimate step in bacillamide D synthesis. Structural analysis of the oxidase reveals a dimeric, two-lobed architecture with a remnant RiPP recognition element and a dramatic wrapping loop. The oxidase forms a stable complex with the NRPS and dimerizes it. We visualized co-complexes of the oxidase bound to the elongation module of the NRPS using X-ray crystallography and cryo-EM. The three active sites (for adenylation, condensation/cyclization, and oxidation) form an elegant arc to facilitate substrate delivery. The structures enabled a proof-of-principle bioengineering experiment in which the BmdC oxidase domain is embedded into the NRPS. | |||||||||
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_23588.map.gz | 398.8 MB | EMDB map data format | |
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Header (meta data) | emd-23588-v30.xml emd-23588.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23588_fsc.xml | 16.7 KB | Display | FSC data file |
Images | emd_23588.png | 147.5 KB | ||
Masks | emd_23588_msk_1.map | 421.9 MB | Mask map | |
Others | emd_23588_half_map_1.map.gz emd_23588_half_map_2.map.gz | 391.5 MB 391.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23588 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23588 | HTTPS FTP |
-Validation report
Summary document | emd_23588_validation.pdf.gz | 560.8 KB | Display | EMDB validaton report |
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Full document | emd_23588_full_validation.pdf.gz | 560.3 KB | Display | |
Data in XML | emd_23588_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | emd_23588_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23588 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23588 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_23588.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | EM Map of the elongation module of the bacillamide NRPS, BmdB, complexed with the oxidase BmdC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.14 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_23588_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half Map B of the elongation module of...
File | emd_23588_half_map_1.map | ||||||||||||
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Annotation | Half Map B of the elongation module of the bacillamide NRPS, BmdB, complexed with the oxidase BmdC | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map A of the elongation module of...
File | emd_23588_half_map_2.map | ||||||||||||
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Annotation | Half Map A of the elongation module of the bacillamide NRPS, BmdB, complexed with the oxidase BmdC | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM map of the elongation module of the bacillamide NRPS, Bmd...
Entire | Name: Cryo-EM map of the elongation module of the bacillamide NRPS, BmdB, complexed with the oxidase BmdC |
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Components |
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-Supramolecule #1: Cryo-EM map of the elongation module of the bacillamide NRPS, Bmd...
Supramolecule | Name: Cryo-EM map of the elongation module of the bacillamide NRPS, BmdB, complexed with the oxidase BmdC type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Thermoactinomyces vulgaris (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 109.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |