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Yorodumi- EMDB-32864: Structure of an assembly-line polyketide synthase module with typ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32864 | |||||||||
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Title | Structure of an assembly-line polyketide synthase module with typical docking domain position | |||||||||
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Sample |
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Keywords | megaenzyme / HYDROLASE | |||||||||
Biological species | Streptomyces chartreusis NRRL 3882cha (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.55 Å | |||||||||
Authors | Wang J / Wang Z | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: C-N bond formation by a polyketide synthase. Authors: Jialiang Wang / Xiaojie Wang / Xixi Li / LiangLiang Kong / Zeqian Du / Dandan Li / Lixia Gou / Hao Wu / Wei Cao / Xiaozheng Wang / Shuangjun Lin / Ting Shi / Zixin Deng / Zhijun Wang / Jingdan Liang / Abstract: Assembly-line polyketide synthases (PKSs) are molecular factories that produce diverse metabolites with wide-ranging biological activities. PKSs usually work by constructing and modifying the ...Assembly-line polyketide synthases (PKSs) are molecular factories that produce diverse metabolites with wide-ranging biological activities. PKSs usually work by constructing and modifying the polyketide backbone successively. Here, we present the cryo-EM structure of CalA3, a chain release PKS module without an ACP domain, and its structures with amidation or hydrolysis products. The domain organization reveals a unique "∞"-shaped dimeric architecture with five connected domains. The catalytic region tightly contacts the structural region, resulting in two stabilized chambers with nearly perfect symmetry while the N-terminal docking domain is flexible. The structures of the ketosynthase (KS) domain illustrate how the conserved key residues that canonically catalyze C-C bond formation can be tweaked to mediate C-N bond formation, revealing the engineering adaptability of assembly-line polyketide synthases for the production of novel pharmaceutical agents. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32864.map.gz | 49.2 MB | EMDB map data format | |
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Header (meta data) | emd-32864-v30.xml emd-32864.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32864_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_32864.png | 78.3 KB | ||
Filedesc metadata | emd-32864.cif.gz | 3.9 KB | ||
Others | emd_32864_additional_1.map.gz emd_32864_half_map_1.map.gz emd_32864_half_map_2.map.gz | 40.7 MB 40.8 MB 40.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32864 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32864 | HTTPS FTP |
-Validation report
Summary document | emd_32864_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_32864_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_32864_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | emd_32864_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32864 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32864 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_32864.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_32864_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_32864_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_32864_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : an assembly-line polyketide synthase module containing KS-AT-DH-K...
Entire | Name: an assembly-line polyketide synthase module containing KS-AT-DH-KR domains |
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Components |
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-Supramolecule #1: an assembly-line polyketide synthase module containing KS-AT-DH-K...
Supramolecule | Name: an assembly-line polyketide synthase module containing KS-AT-DH-KR domains type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Streptomyces chartreusis NRRL 3882cha (bacteria) |
Molecular weight | Theoretical: 0.36 kDa/nm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
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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 (6k x 4k) / Average electron dose: 48.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |