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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | CalA3 with hydrolysis product | |||||||||
![]() | postprocessed map | |||||||||
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![]() | polyketide synthase / BIOSYNTHETIC PROTEIN / TRANSFERASE | |||||||||
Function / homology | ![]() beta-ketoacyl-[acyl-carrier-protein] synthase I / DIM/DIP cell wall layer assembly / fatty acid synthase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.97 Å | |||||||||
![]() | Wang J / Wang Z | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 9.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.9 KB 17.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.7 KB | Display | ![]() |
Images | ![]() | 108.8 KB | ||
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() ![]() | 167.9 MB 169.9 MB 169.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 791.5 KB | Display | ![]() |
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Full document | ![]() | 791.1 KB | Display | |
Data in XML | ![]() | 21 KB | Display | |
Data in CIF | ![]() | 27.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8i4zMC ![]() 7wvzC ![]() 8i4yC 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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Annotation | postprocessed map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.89 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: full map
File | emd_35189_additional_1.map | ||||||||||||
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Annotation | full map | ||||||||||||
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-Half map: half map 1
File | emd_35189_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
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-Half map: half map 2
File | emd_35189_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
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Sample components
-Entire : CalA3, a polyketide synthase catalyzing C-N bond formation
Entire | Name: CalA3, a polyketide synthase catalyzing C-N bond formation |
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Components |
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-Supramolecule #1: CalA3, a polyketide synthase catalyzing C-N bond formation
Supramolecule | Name: CalA3, a polyketide synthase catalyzing C-N bond formation type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Beta-ketoacyl-acyl-carrier-protein synthase I
Macromolecule | Name: Beta-ketoacyl-acyl-carrier-protein synthase I / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 178.383562 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MPDEEKLQKY LRKVTAELQQ ARRRLAAAES QSQEPIAVLG IGCRFPGGVR SPEDLWDLVD SGGDAVGGLP AGRGWQAGSA LDGVNAGFI HGVEEFDPYF FGLDPVEAAA MDPQQRLLLE TTWEAFERAG IDPVAARGSR TAVYAGVQFG GYPLLMREAP P PQVLDHLG ...String: MPDEEKLQKY LRKVTAELQQ ARRRLAAAES QSQEPIAVLG IGCRFPGGVR SPEDLWDLVD SGGDAVGGLP AGRGWQAGSA LDGVNAGFI HGVEEFDPYF FGLDPVEAAA MDPQQRLLLE TTWEAFERAG IDPVAARGSR TAVYAGVQFG GYPLLMREAP P PQVLDHLG LGNSVGAASG RLAYQFGLLG GAVTVDTQCT SSIVALHLAV KALRNGECAL ALAGGACVMS LPTVLMDFHR RS LLAPDGR SKSFAAAADG VSLAEGAGML LLERLSDARR NGHPVMAVIR GTAINQDGAT NGIISPSGRA QERVIRAALA DGR VTADSV DAVEGHGVGA TLGDGVEVTS LLSTYGQERP AGRPLLLGSV KSNIGHTQTV GAVAGIVKLV MALRNERLPR TVHV DGPTP HADWSSGTVR LLTEPEPWRR GERVRRAGLT CLTLSGTNGH LILEEPPADE PAARPANPER TVPLVLSAKS PTALR EQAE RLRATITAAE PVDVGHSLHT TRSSFRHRAV VLGTGREELA AGLDALAGDR TADGLVRGVA RAQGQTALLF GGAGDG TSG DRPADAEGPR TARGLYEAFP AFAEALDEVT EHLAGLLGPE VRAAVREPGP ACAEPTVVGQ AVAFALNTAL HRLLTAF AV RPDATLGHGA GEVAAAYAAG ALSLADGAAL VTALGRITER VATGPGASVW VRATEDEVRA ALSGSQEQVG AAVAAVDE P GTTVVSGDAG AVARVAAHWR AHGRATGAPR PARLLLSPDD EQAALAELRA IVAGLAFREP EVPLLSTVTG QPVEPAELR SAEHWLDHLR GPTRFLDGVR RLRTDGVTRL VGLDLSGDLT GPAGRSAAGF GEPGRPLLLA SVPGGGRPPG QALLSALGEL HTDGVAIDW SQAFEGRGAR RVDLPTYPYQ KVRCWLVPPE PQVSVVAAPP HPLLGTALDL VDATGQSFTQ QLTPGQVAGV F GQQLYGTP VLPAGARLEW LLAAARHGSP DSAWTLTGIR LPGTVSAASG TPVALQTSRE DSGDGHRVRA FVKGPGTGGG RW AERGGAT VVPAVTRPAP DRVDPESLPE GLAELDVAEV YRRLWRQGSD YAEPLRVLRR VWLGGDEAVA LVGTADVPTG PSG WSRWAA VLEAAVQLAA LSGSGPRTPV SVDRLEVSGP PSEVVWLRVR HGADGAADAV VLSGEGVRLA AVQGLRLRPM AGRE PAGLA EAPLERHEVV WHALAEDGRP GAIGGGTGSW LVFSDDPERA AAWCDELALF GVPAVALAGE DAEGRDGTET VPVGT GDPD VVGKTFAELR ERGVTVAGLL VHDAGDAREP ASGADDPLDA ACRRGGRTLA LVRGFLQEYA EQTPRIVLCS AGAAAG LAG GPPHPAQAPL TALFTSLVWE HPELPCAQVD LDPAEDPPTV VSLLGQVMRL PGAGRLAVRG GRWFEARLER RPAPADR GE RLALRPDATY LVAGGDTRHA AAALEWLAAR GARSVVLAGA ESERGDLAGA RTTGHAGIER LEHVAVDLSS AADVARLA E LCADGRPPLR GVLLLPQPVA GGGLDELDGA RFGAELAGAL RGPVELTRRF TDVGLTGGTD FFVLSTSVVS LPGRAGTVV GSAADAFLTA LARHHRQAGL PVVAAAWGPW LESVDESDEA PAVAFAEAGV YPAPGGEMLD ALLPLPAAGE ADGSGEAGLA RVDWDRYLT AGHRPLPYTV LETRASYDEE KAPGFGQNRM UniProtKB: Beta-ketoacyl-acyl-carrier-protein synthase I |
-Macromolecule #2: 11-oxidanylidene-11-(1~{H}-pyrrol-2-yl)undecanoic acid
Macromolecule | Name: 11-oxidanylidene-11-(1~{H}-pyrrol-2-yl)undecanoic acid type: ligand / ID: 2 / Number of copies: 1 / Formula: ONF |
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Molecular weight | Theoretical: 265.348 Da |
Chemical component information | ![]() ChemComp-ONF: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 4.5 mg/mL |
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Buffer | pH: 7.9 |
Grid | Model: C-flat-1.2/1.3 / Material: GOLD |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.06 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |