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- EMDB-38411: Cryo-EM structure of colibactin assembly line polyketide synthase... -

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Basic information

Entry
Database: EMDB / ID: EMD-38411
TitleCryo-EM structure of colibactin assembly line polyketide synthase ClbI KS-AT didomain crosslinked with its precursor module, ClbH
Map data
Sample
  • Complex: ClbH-bound ClbI
    • Protein or peptide: Polyketide synthase
    • Protein or peptide: Peptide synthetase
    • Protein or peptide: polypeptide from ClbH
Keywordscolibactin / microbiome / polyketide synthase / colorectal cancer / NRPS-PKS hybrid / BIOSYNTHETIC PROTEIN / TRANSFERASE
Function / homology
Function and homology information


ligase activity, forming carbon-sulfur bonds / beta-ketoacyl-[acyl-carrier-protein] synthase I / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / membrane / cytoplasm
Similarity search - Function
Condensation domain / Condensation domain / Amino acid adenylation domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / ANL, N-terminal domain / : / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain ...Condensation domain / Condensation domain / Amino acid adenylation domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / ANL, N-terminal domain / : / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Acyl transferase/acyl hydrolase/lysophospholipase / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / AMP-binding enzyme, C-terminal domain superfamily / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Peptide synthetase / Polyketide synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsKim M / Kim J / Kang JY
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF- 2019M3E5D6063908 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF- 2020R1F1A107746211 Korea, Republic Of
CitationJournal: Structure / Year: 2025
Title: Cryo-EM structures of human microbiome-derived polyketide synthases that assemble genotoxic colibactin
Authors: Kim M / Kim J / Olinares PDB / Park J / Chait BT / Kang JY
History
DepositionDec 22, 2023-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38411.png

Downloads & links

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Map

FileDownload / File: emd_38411.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.091 Å		1.09 Å/pix.
x 256 pix.
= 279.091 Å		1.09 Å/pix.
x 256 pix.
= 279.091 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0902 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026
Minimum - Maximum-0.1634524 - 0.27775815
Average (Standard dev.)0.00006161421 (±0.0062799244)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 279.0912 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38411_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38411_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38411_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : ClbH-bound ClbI

EntireName: ClbH-bound ClbI
Components
  • Complex: ClbH-bound ClbI
    • Protein or peptide: Polyketide synthase
    • Protein or peptide: Peptide synthetase
    • Protein or peptide: polypeptide from ClbH

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Supramolecule #1: ClbH-bound ClbI

SupramoleculeName: ClbH-bound ClbI / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 360 KDa

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Macromolecule #1: Polyketide synthase

MacromoleculeName: Polyketide synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: beta-ketoacyl-[acyl-carrier-protein] synthase I
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 99.125695 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAENDFGIAI IGMAGRFPQA DTVQAFWENL LASRECISFY SDEELLAMGI SPEFVQHPDY VKAKGEVADI DKFDAAFFGI APREAELMD PQHRVLLETA WAAFEDAGYV AADYPGDVGI FAGKSMDSYL MLNLMPHFKR VFSSGSLQAA IGNDKDSITT T IAYHLNLR ...String:
MAENDFGIAI IGMAGRFPQA DTVQAFWENL LASRECISFY SDEELLAMGI SPEFVQHPDY VKAKGEVADI DKFDAAFFGI APREAELMD PQHRVLLETA WAAFEDAGYV AADYPGDVGI FAGKSMDSYL MLNLMPHFKR VFSSGSLQAA IGNDKDSITT T IAYHLNLR GPAITVQTSS STSLVAVCVA CQSLLTWQCD MAIAGGVTLG PPAKTGYLSQ EGGITAADGH CRAFSDNSSG FV PGTGAGL VVLKRVDEAL RDGDNIYAVI KGFAVNNDGS EKISYTAPSV DAQARAIAQA QRLAGLTPQD ITYVEAHGTG TRL GDPVEF SALSQAFAGA SQKQYCALGS VKTNIGHLDT AAGVAGLIKT ALAVQQGIIP ATLHFERPNA QIDLTNSPFY INTT CQPWQ PESGIRRAGV TSLGMGGTNA HVVLEQAPAV DLQARAPVPA YSILPFSAKT DSALSSGLAR FADFLQHESL PDRRD LAWT LSQGRKAFAH RAALVTRDLH AAGTLLQQAA TAPFARGVAQ TQLGLGLLFS GQGSQYQRMG HQLYQVWPAY ADAFDR CAT LLEREYQLDI RHELFRAEVS LAQGERLAQT CLTQPLLFSV EYALAQLWLS WGITPTVMIG HSLGEWVAAT LAGVFSL ED ALRLVARRAE LMHQAPSGAM LMVALPEAQI RALITAPLAI AAVNAPDYSV IAGPTSEILA VSQRLTEQNI INKRLHTS H AFHSSMMQDA AQALRQAFEN VRLNPPTLTI ISTVTGAHVS ADTLTTPDYW IEQMLMPVQF SAALQEAQAT FDVDFLEIG PGATLTQLTN GHALGDRLAF SSLPAGARSS DEHKHILDTV AALWVRGHNI DLSAFAGEQP RRVSLPTYAF DKIRYWVDSP EEQRSAVTP VADAGSKLSS GLEVLFQGPS SGHHHHHHHH HH

UniProtKB: Polyketide synthase

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Macromolecule #2: Peptide synthetase

MacromoleculeName: Peptide synthetase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 180.781828 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSEFMEQQ GIMRQLPTDD QTIVDYLYRI AGEYGEKAAV LMGDAALSYH DLNARSNQL AHYLRGLGIG EDRVVAIRLP RGMAMLIAIF AIVKAGGAYL PLAYNAPRSR IENILSNSGA VCLIGTDDGD R WPIPRVEI ...String:
MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSEFMEQQ GIMRQLPTDD QTIVDYLYRI AGEYGEKAAV LMGDAALSYH DLNARSNQL AHYLRGLGIG EDRVVAIRLP RGMAMLIAIF AIVKAGGAYL PLAYNAPRSR IENILSNSGA VCLIGTDDGD R WPIPRVEI DSAAVSAMPT TDLRYRPHAR QLAYIIYTSG STGVPKGVAT EHAALLNRIV WMQNAYPISS QDVLFQKTVY TF DVSVWEM FWWAMYGASV VLLPSGLESD PRTLARLIQR HRVSVVHFVP SMLNLFVEYL EMKQDPRLTA SLRLVFSSGE KLT VHSVAR FYQSVAQGDL INLYGPTEAA IDVSHHRCLR GYDYDDIPIG QAIDGCRLYV LDDHGNPVAD GEEGELYLAG IGLA RGYLN NVALTDRCFT IHPTLRHLGK PERLYKTGDL VWRDGESQQI HYIGRNDFQI KIRGLRVELG EIEAHAMRFP GVQQA VVVA DQDDPDNQLI YAFVVSSVPL NLAALMDALS KNLPAYMLPN RLLAMSELPL SDNGKCCRKT LLDLARAYSA SRVDLR ETP AVRYLPLSSA QSSMWFMQQL APHTALYNNP TALLLEGELD RTRMDGAIRQ LMSRHTLLRA MAETHNGQPV LAVPQCV SS QALLTIVPLP SVSDDNALQA MINQRAAHPM PLTSGTPLCR FELLTLDDDR SVLLIHLHHI ISDGWSKGVL LRELQAAY N GESLTPEPLL EYADYMEYQE EWRQSDAYQD AMRYWQNTLA GTLPILDIPT DQPRQKVARY QGAFVAFALS ANTCERVLA AARAQRVSLY NYLLTAFVLL LHRNARQQEY IVGMPIAARL TKEQEHMIAP LVNVLPLRLP LDEAASFSEL VQTIRGILFA AFRHQRLEF TDIVRAVNVD RSAGHFPIYQ CMFQLDNMPL ASPTLNGVNV TPLLLDTSAS QVDISLSMQH IDGRITGTFE Y DAGLYSAD RIQHLVAQWR ELLDEASSQP TQLVRDLIRF TPREHAWLAR HNATEVALPP VDNLLALVLP HCQQRPTQVA LR HADDAMT YGELQQATMQ MCTWLRAQGV KRGESVALQL PFCFELIIAQ LAILSLGASY VPLDGNAPAA RNALILAQAT PCM LLVAQP LESPHGLTIP WVLVPDWRSL LTEIPNLPVS VAPDALDCDA VVIFTSGTTG QPKGVRLSQR NLVNLTASFI SSYQ VTHQD VLLPITSVAS ASFVGEVLPL LAAGGTLVLA QKAQSLDSDA LIALLASQRV TILSTTPSLS ASLSVLAQSM GSLRL FLCG GEALEYEQIA PLLPHMAVVN GYGLTESGIC STYFPVAKRR EQETGALPIG RPIQNTQAYV VDAYNRLVPP GACGEL CFS GLGISPGYLD ARQDPERFVE LPEYPGVRVL KTGDRARWAT DGMLFYLGRQ DRQVQIRGYR VELGDIESLL KQHPDIA DA WVDVRRNAAA TPLLVAFYCS VNGVALDAQQ LRVWLSLRLP LHMLPLLYVP LSAMPLGVNG KIDPQCLPLV DLRQLEGP G EYVPPATELE QRLAEIWQQL LGLERVGTTT NFFDLGGHSL LLVQMQQYIG QQCGQHVALV DLLRFTTIKR LAEFLLAPD AAQGTTGDQT QLRAAKQRLA FGHTRWAATT DSHH

UniProtKB: Peptide synthetase

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Macromolecule #3: polypeptide from ClbH

MacromoleculeName: polypeptide from ClbH / type: protein_or_peptide / ID: 3
Details: unknown residue range, alpha-helical polypeptide chain derived from the ClbH C-terminal motif
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 2.230741 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.50 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
20.0 mMTris-HClTRIS-hydrochloride
10.0 mMMgCl2magnesium chloride
1.0 mMDTTdithiothreitol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 2.6 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 6000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 2 / Number real images: 7283 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen 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

Particle selectionNumber selected: 2099741
CTF correctionSoftware - Name: cryoSPARC (ver. 3.0.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab-initio reconstruction
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 246050
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 106098 / Software - Name: RELION (ver. 3.1.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8xjz:
Cryo-EM structure of colibactin assembly line polyketide synthase ClbI KS-AT didomain crosslinked with its precursor module, ClbH

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