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- EMDB-38222: Cryo-EM structure of colibactin assembly line polyketide synthase... -
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Open data
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Basic information
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Title | Cryo-EM structure of colibactin assembly line polyketide synthase ClbC (apo state) | |||||||||
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![]() | colibactin / microbiome / polyketide synthase / colorectal cancer / NRPS-PKS hybrid / BIOSYNTHETIC PROTEIN | |||||||||
Function / homology | ![]() DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.06 Å | |||||||||
![]() | Kim J / Kim M / Kang JY | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural study on human microbiome-derived polyketide synthases that assemble genotoxic colibactin. Authors: Minjae Kim / Jinwoo Kim / Gyu Sung Lee / Paul Dominic B Olinares / Yougant Airan / Jasmine L Chow / Jongseok Park / Yujin Jeong / Jiho Park / Brian T Chait / Seth B Herzon / Chung Sub Kim / Jin Young Kang / ![]() ![]() Abstract: Colibactin, a human microbiome-derived genotoxin, promotes colorectal cancer by damaging the host gut epithelial genomes. While colibactin is synthesized via a hybrid non-ribosomal peptide synthetase ...Colibactin, a human microbiome-derived genotoxin, promotes colorectal cancer by damaging the host gut epithelial genomes. While colibactin is synthesized via a hybrid non-ribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) pathway, known as pks or clb, the structural details of its biosynthetic enzymes remain limited, hindering our understanding of its biosynthesis and clinical application. In this study, we report the cryo-EM structures of two colibactin-producing PKS enzymes, ClbC and ClbI, captured in different reaction states using a substrate-mimic crosslinker. Our structural analysis revealed the binding sites of carrier protein (CP) domains of the ClbC and ClbI on their ketosynthase (KS) domains. Further, we identified a novel NRPS-PKS docking interaction between ClbI and its upstream enzyme, ClbH, mediated by the C-terminal peptide ClbH and the dimeric interface of ClbI, establishing a 1:2 stoichiometry. These findings advance our understanding of colibactin assembly line and provide broader insights into NRPS-PKS natural product biosynthesis mechanisms. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 166.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22 KB 22 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 36.5 KB | ||
Masks | ![]() | 178 MB | ![]() | |
Filedesc metadata | ![]() | 7.2 KB | ||
Others | ![]() ![]() | 140.8 MB 141.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1005.6 KB | Display | ![]() |
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Full document | ![]() | 1005.1 KB | Display | |
Data in XML | ![]() | 20.1 KB | Display | |
Data in CIF | ![]() | 26.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8xblMC ![]() 8xjtC ![]() 8xjuC ![]() 8xjyC ![]() 8xjzC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
-Entire : apo-ClbC
Entire | Name: apo-ClbC |
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Components |
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-Supramolecule #1: apo-ClbC
Supramolecule | Name: apo-ClbC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 100 KDa |
-Macromolecule #1: Colibactin polyketide synthase ClbC
Macromolecule | Name: Colibactin polyketide synthase ClbC / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 99.302961 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSEFELRR QALEYASEMN GMEIAIIGMA VRFPQSRTLH EFWHNIVQGK ECVTFFSEE ELLAEGVEQS TLDNPAYVRA KPYIEGICDF DAAFFGYSHK EAQTLDPKSR VLHEVAYHAL EDAGYAQRTS D LITGVFVG ...String: MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSEFELRR QALEYASEMN GMEIAIIGMA VRFPQSRTLH EFWHNIVQGK ECVTFFSEE ELLAEGVEQS TLDNPAYVRA KPYIEGICDF DAAFFGYSHK EAQTLDPKSR VLHEVAYHAL EDAGYAQRTS D LITGVFVG ASEDVDWLRR SLSQIGGDAL NRFESGIYGH KDLLAHLIAY SLNLNGPVYS LYTSCSTSLS ATHIACRSLL FG ECDLALA GGITIDLPQK SGYFCQQGMI HSTDGHCRPF DSQASGTLFG DGAGVVVLRR LEDALAAGDR IYAVIRGSAV NND GKQKIG FVAPGHEGQK AVICAACHLA EVSPESIGYV ETHGTGTRIG DPIEFAALTE AFDTSHRQYC ALGAVKANIG HTHA AAGVA GLIKTALVLH HRTIPPLANY QMPNSKLDLA HSPFYIPIQP QEWPASRMPP RAGVSSFGIG GTNVHMILEG LNPAV RDDH DQVRAPVFIP LSAPSFEQLD ELTQQLTPLL ATLDASTLAY TQQVARPVFD CRRVIQVEND GTQAMLASLD NLMPDA PWG LHCPDLRTTN DCTYAQWLAH SAHYQREATA LTALLDGMNI PPAYCHAETW AAQANSSLLI RGCQTIAALK TWMNLLP TL TLLSGAGTGL LPAAAASGMI ATQDVLHLLW EMEQKALHLW LPERHEPIPG YVLAWQGNPI TDAQRNDRGF WSEALLAD T RELGEGVHSI NWVRLPPEIR EDVDVLRYVA QLWCAGINVD WAVWYGTPLP QRGSASAYPF AHNHYPLPGR VMGSVETQP EAGPETHHPY QARPVLSVPF VAAHSRGMQY ITGLMELLLE ISPVGVDDDF FELGGHSLLV TQLTSRLERD FNVHIDLLTL MENPNPRNI YAHIAAQLGG EDNLEIACQ UniProtKB: Colibactin polyketide synthase ClbC |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa / Details: negative | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 6000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 1 / Number real images: 12611 / Average exposure time: 2.3 sec. / Average electron dose: 58.85 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-8xbl: |