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Yorodumi- EMDB-41307: KS-AT core of 6-deoxyerythronolide B synthase (DEBS) Module 3 cro... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41307 | |||||||||||||||
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Title | KS-AT core of 6-deoxyerythronolide B synthase (DEBS) Module 3 crosslinked with its elongation ACP partner | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | polyketide synthase / antibody / BIOSYNTHETIC PROTEIN | |||||||||||||||
Function / homology | Function and homology information macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Saccharopolyspora erythraea (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.71 Å | |||||||||||||||
Authors | Cogan DP / Soohoo AM / Chen M / Brodsky KL / Liu Y / Khosla C | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Nat Chem Biol / Year: 2024 Title: Structural basis for intermodular communication in assembly-line polyketide biosynthesis. Authors: Dillon P Cogan / Alexander M Soohoo / Muyuan Chen / Yan Liu / Krystal L Brodsky / Chaitan Khosla / Abstract: Assembly-line polyketide synthases (PKSs) are modular multi-enzyme systems with considerable potential for genetic reprogramming. Understanding how they selectively transport biosynthetic ...Assembly-line polyketide synthases (PKSs) are modular multi-enzyme systems with considerable potential for genetic reprogramming. Understanding how they selectively transport biosynthetic intermediates along a defined sequence of active sites could be harnessed to rationally alter PKS product structures. To investigate functional interactions between PKS catalytic and substrate acyl carrier protein (ACP) domains, we employed a bifunctional reagent to crosslink transient domain-domain interfaces of a prototypical assembly line, the 6-deoxyerythronolide B synthase, and resolved their structures by single-particle cryogenic electron microscopy (cryo-EM). Together with statistical per-particle image analysis of cryo-EM data, we uncovered interactions between ketosynthase (KS) and ACP domains that discriminate between intra-modular and inter-modular communication while reinforcing the relevance of conformational asymmetry during the catalytic cycle. Our findings provide a foundation for the structure-based design of hybrid PKSs comprising biosynthetic modules from different naturally occurring assembly lines. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41307.map.gz | 171.2 MB | EMDB map data format | |
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Header (meta data) | emd-41307-v30.xml emd-41307.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
Images | emd_41307.png | 27.7 KB | ||
Filedesc metadata | emd-41307.cif.gz | 6.6 KB | ||
Others | emd_41307_half_map_1.map.gz emd_41307_half_map_2.map.gz | 318.2 MB 318.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41307 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41307 | HTTPS FTP |
-Validation report
Summary document | emd_41307_validation.pdf.gz | 959.3 KB | Display | EMDB validaton report |
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Full document | emd_41307_full_validation.pdf.gz | 958.9 KB | Display | |
Data in XML | emd_41307_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | emd_41307_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41307 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41307 | HTTPS FTP |
-Related structure data
Related structure data | 8tjpMC 8tjnC 8tjoC 8tkoC 8tpwC 8tpxC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41307.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.946 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41307_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41307_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : KS-AT core of DEBS Module 3 crosslinked with its elongation ACP p...
Entire | Name: KS-AT core of DEBS Module 3 crosslinked with its elongation ACP partner |
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Components |
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-Supramolecule #1: KS-AT core of DEBS Module 3 crosslinked with its elongation ACP p...
Supramolecule | Name: KS-AT core of DEBS Module 3 crosslinked with its elongation ACP partner type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharopolyspora erythraea (bacteria) |
Molecular weight | Theoretical: 210 KDa |
-Macromolecule #1: EryAII
Macromolecule | Name: EryAII / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharopolyspora erythraea (bacteria) |
Molecular weight | Theoretical: 99.76575 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MVTDSEKVAE YLRRATLDLR AARQRIRELE SDPIAIVSMA CRLPGGVNTP QRLWELLREG GETLSGFPTD RGWDLARLHH PDPDNPGTS YVDKGGFLDD AAGFDAEFFG VSPREAAAMD PQQRLLLETS WELVENAGID PHSLRGTATG VFLGVAKFGY G EDTAAAED ...String: MVTDSEKVAE YLRRATLDLR AARQRIRELE SDPIAIVSMA CRLPGGVNTP QRLWELLREG GETLSGFPTD RGWDLARLHH PDPDNPGTS YVDKGGFLDD AAGFDAEFFG VSPREAAAMD PQQRLLLETS WELVENAGID PHSLRGTATG VFLGVAKFGY G EDTAAAED VEGYSVTGVA PAVASGRISY TMGLEGPSIS VDTACSSSLV ALHLAVESLR KGESSMAVVG GAAVMATPGV FV DFSRQRA LAADGRSKAF GAGADGFGFS EGVTLVLLER LSEARRNGHE VLAVVRGSAL NQDGASNGLS APSGPAQRRV IRQ ALESCG LEPGDVDAVE AHGTGTALGD PIEANALLDT YGRDRDADRP LWLGSVKSNI GHTQAAAGVT GLLKVVLALR NGEL PATLH VEEPTPHVDW SSGGVALLAG NQPWRRGERT RRAAVSAFGI SGTNAHVIVE EAPEREHRET TAHDGRPVPL VVSAR STAA LRAQAAQIAE LLERPDADLA GVGLGLATTR ARHEHRAAVV ASTREEAVRG LREIAAGAAT ADAVVEGVTE VDGRNV VFL FPGQGSQWAG MGAELLSSSP VFAGKIRACD ESMAPMQDWK VSDVLRQAPG APGLDRVDVV QPVLFAVMVS LAELWRS YG VEPAAVVGHS QGEIAAAHVA GALTLEDAAK LVVGRSRLMR SLSGEGGMAA VALGEAAVRE RLRPWQDRLS VAAVNGPR S VVVSGEPGAL RAFSEDCAAE GIRVRDIDVD YASHSPQIER VREELLETTG DIAPRPARVT FHSTVESRSM DGTELDARY WYRNLRETVR FADAVTRLAE SGYDAFIEVS PHPVVVQAVE EAVEEADGAE DAVVVGSLHR DGGDLSAFLR SMATAHVSGV DIRWDVALP GAAPFALPTY PFQRKRYWLQ PAAPAAASDE LAYRSSSVDK LAAALEHHHH HH UniProtKB: EryAII |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 8 mg/mL | ||||||||||||
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Buffer | pH: 7.2 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 11 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 30 s glow, 10 s hold, 15 mA | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 4601 / Average exposure time: 6.45 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 150.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |