+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5653 | |||||||||
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Title | Cryo-EM structure of MeMal-PikAIII | |||||||||
Map data | Reconstruction of the 5th module from the pikromycin biosynthetic pathway (PikAIII) incubated with methylmalonyl-CoA. | |||||||||
Sample |
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Keywords | Type I polyketide synthase module | |||||||||
Function / homology | Function and homology information 10-deoxymethynolide synthase / narbonolide synthase / macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / acyltransferase activity, transferring groups other than amino-acyl groups / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / identical protein binding ...10-deoxymethynolide synthase / narbonolide synthase / macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / acyltransferase activity, transferring groups other than amino-acyl groups / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Streptomyces venezuelae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.3 Å | |||||||||
Authors | Dutta S / Whicher JR / Hansen DA / Hale WA / Chemler JA / Narayan AR / Hakansson K / Sherman DH / Smith JL / Skiniotis G | |||||||||
Citation | Journal: Nature / Year: 2014 Title: Structure of a modular polyketide synthase. Authors: Somnath Dutta / Jonathan R Whicher / Douglas A Hansen / Wendi A Hale / Joseph A Chemler / Grady R Congdon / Alison R H Narayan / Kristina Håkansson / David H Sherman / Janet L Smith / Georgios Skiniotis / Abstract: Polyketide natural products constitute a broad class of compounds with diverse structural features and biological activities. Their biosynthetic machinery, represented by type I polyketide synthases ...Polyketide natural products constitute a broad class of compounds with diverse structural features and biological activities. Their biosynthetic machinery, represented by type I polyketide synthases (PKSs), has an architecture in which successive modules catalyse two-carbon linear extensions and keto-group processing reactions on intermediates covalently tethered to carrier domains. Here we used electron cryo-microscopy to determine sub-nanometre-resolution three-dimensional reconstructions of a full-length PKS module from the bacterium Streptomyces venezuelae that revealed an unexpectedly different architecture compared to the homologous dimeric mammalian fatty acid synthase. A single reaction chamber provides access to all catalytic sites for the intramodule carrier domain. In contrast, the carrier from the preceding module uses a separate entrance outside the reaction chamber to deliver the upstream polyketide intermediate for subsequent extension and modification. This study reveals for the first time, to our knowledge, the structural basis for both intramodule and intermodule substrate transfer in polyketide synthases, and establishes a new model for molecular dissection of these multifunctional enzyme systems. | |||||||||
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_5653.map.gz | 24.2 MB | EMDB map data format | |
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Header (meta data) | emd-5653-v30.xml emd-5653.xml | 12 KB 12 KB | Display Display | EMDB header |
Images | 400_5653.gif 80_5653.gif | 43.2 KB 3.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5653 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5653 | HTTPS FTP |
-Validation report
Summary document | emd_5653_validation.pdf.gz | 78.5 KB | Display | EMDB validaton report |
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Full document | emd_5653_full_validation.pdf.gz | 77.6 KB | Display | |
Data in XML | emd_5653_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5653 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5653 | HTTPS FTP |
-Related 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_5653.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the 5th module from the pikromycin biosynthetic pathway (PikAIII) incubated with methylmalonyl-CoA. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : MeMal-PikAIII
Entire | Name: MeMal-PikAIII |
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Components |
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-Supramolecule #1000: MeMal-PikAIII
Supramolecule | Name: MeMal-PikAIII / type: sample / ID: 1000 Details: Sample was not frozen prior to loading on the grid. The sample was monodisperse. Oligomeric state: Dimer / Number unique components: 2 |
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Molecular weight | Experimental: 328 KDa / Theoretical: 328 KDa / Method: Gel filtration chromatography |
-Macromolecule #1: PikAIII
Macromolecule | Name: PikAIII / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes |
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Source (natural) | Organism: Streptomyces venezuelae (bacteria) |
Molecular weight | Experimental: 328 KDa / Theoretical: 328 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET28b |
Sequence | UniProtKB: Narbonolide/10-deoxymethynolide synthase PikA3, module 5 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.4 / Details: 50 mM HEPES, 100mM NaCl |
Grid | Details: Glow-discharged Quantifoil R2/200 mesh grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 89 K / Instrument: FEI VITROBOT MARK IV Method: Blot for 1.5-2.0 seconds before plunging (3 microliter sample). |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Min: 89 K / Max: 89 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 135,000 times magnification. |
Date | Jun 15, 2011 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 310 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 66964 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | The particles were selected manually. |
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CTF correction | Details: Each micrograph |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN1, EMAN2 / Number images used: 56292 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 3
Initial model | PDB ID: |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |