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- EMDB-45812: Modifying region of EcPKS1 -

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Basic information

Entry
Database: EMDB / ID: EMD-45812
TitleModifying region of EcPKS1
Map dataSharpened Map to 3.5A for C-terminal modifying region of EcPKS1
Sample
  • Complex: modifying region of homodimer of EcPKS1
    • Protein or peptide: Polyketide synthase 1
Keywordspolyketide adenosyl transferase / beta-keto-synthase dehydratase / keto-reductase / Acyl carrier protein / BIOSYNTHETIC PROTEIN
Biological speciesElysia chlorotica (eastern emerald elysia)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSchubert HL / Hill CP
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2203613 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: The structure of full-length AFPK supports the ACP linker in a role that regulates iterative polyketide and fatty acid assembly.
Authors: Heidi L Schubert / Feng Li / Christopher P Hill / Eric W Schmidt /
Abstract: The polyketide synthases (PKSs) in microbes and the cytoplasmic fatty acid synthases in humans (FASs) are related enzymes that have been well studied. As a result, there is a paradigm explaining in ...The polyketide synthases (PKSs) in microbes and the cytoplasmic fatty acid synthases in humans (FASs) are related enzymes that have been well studied. As a result, there is a paradigm explaining in general terms how FASs repeatedly use a set of enzymatic domains to produce simple fats, while PKSs use the domains in a much more complex manner to produce pharmaceuticals and other elaborate molecules. However, most animals also have PKSs that do not conform to the rules described in microbes, including a large family of enzymes that bridge fatty acid and polyketide metabolism, the animal FAS-like PKSs (AFPKs). Here, we present the cryoelectron microscopy structures of two AFPKs from sea slugs. While the AFPK resemble mammalian FASs, their chemical products mimic those of PKSs in complexity. How then does the architecture of AFPKs facilitate this structural complexity? Unexpectedly, chemical complexity is controlled not solely by the enzymatic domains but is aided by the dynamics of the acyl carrier protein (ACP), a shuttle that moves intermediates between these domains. We observed interactions between enzyme domains and the linker-ACP domain, which, when manipulated, altered the kinetic properties of the enzyme to change the resulting chemical products. This unveils elaborate mechanisms and enzyme motions underlying lipid and polyketide biochemistry across the domains of life.
History
DepositionJul 19, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45812.png

Downloads & links

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Map

FileDownload / File: emd_45812.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened Map to 3.5A for C-terminal modifying region of EcPKS1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 512 pix.
= 271.36 Å		0.53 Å/pix.
x 512 pix.
= 271.36 Å		0.53 Å/pix.
x 512 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.53 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0229
Minimum - Maximum-0.12393858 - 0.22568218
Average (Standard dev.)0.0008218745 (±0.0077398587)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45812_msk_1.map
Projections & Slices
AxesZYX

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Additional map: unsharpened map

Fileemd_45812_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half B

Fileemd_45812_half_map_1.map
AnnotationHalf B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half A

Fileemd_45812_half_map_2.map
AnnotationHalf A
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : modifying region of homodimer of EcPKS1

EntireName: modifying region of homodimer of EcPKS1
Components
  • Complex: modifying region of homodimer of EcPKS1
    • Protein or peptide: Polyketide synthase 1

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Supramolecule #1: modifying region of homodimer of EcPKS1

SupramoleculeName: modifying region of homodimer of EcPKS1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Elysia chlorotica (eastern emerald elysia)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Polyketide synthase 1

MacromoleculeName: Polyketide synthase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Elysia chlorotica (eastern emerald elysia)
Molecular weightTheoretical: 249.323984 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MAPNNTQQEE ASKGGNSSPE AYLPYSGDIA IAGISGRYPE SDSVGEFRDN LFGKVNMLTC DDRRWKLGHL DLPDVLGKLR SVDRFDSEF FNLNSKQTEM LDPQTRLLLE VCYEAIVDAG ESLASVKGSR TGMYLAISSS EPEQAWICRQ DPYIVMGCPH T MSPNRISF ...String:
MAPNNTQQEE ASKGGNSSPE AYLPYSGDIA IAGISGRYPE SDSVGEFRDN LFGKVNMLTC DDRRWKLGHL DLPDVLGKLR SVDRFDSEF FNLNSKQTEM LDPQTRLLLE VCYEAIVDAG ESLASVKGSR TGMYLAISSS EPEQAWICRQ DPYIVMGCPH T MSPNRISF FFDLHGPSIA YDTACSSVLV ALEAAFQHMR TGVIDSAIVA GVNTCFRALT SKVYQNMGML GPEACKAFDS SG NGYARSE IVSALFLKKS SDSKRIYCSV VNVKTNNDGF TPQGLTFPSG EIQEQLMRNV YADCKLNPKE VSYFECHGTG TPA GDPQET NAIYRVMCTP DKREPLLIGS VKSNMGHAET GSAMASITKV ILAMHEGFIA PNLHFRSPNP KIEGLRDGKM AVVT EATPW SGGYMAINSF GMGGSNAHAV LRSYDVSSSK PHPSAHKPRL FTYSARTEHG LRAILREAQT HAASMEFHAL CQASA DAPL GSMPYRGATI LNGQHDFEVV EKCKSKAREV WFIYAGMGSQ WVGMARCLMQ LDVFRHSLEK SAAVLKPHGV DLLNIL SEG TEDTLRTILN PFVCITSIQV ALTDLLWSMG IRPDGIVGHS MGEVGCAYCD GCLTAEEAVL TAYWRGKCVT DGKVPPG KM AAVGLTWEEA KSQCPAGVVP ACHNAEDSVT ISGAADVMLK FMEELKAKDV FVREVNSSNI AYHSYFMENI YASLKDSL S KVISPKPRTA RWLPTSVPEE LWDSAPAQSS SAEFHANNLV SPVLFHEALQ KIPPTAIAIE LAPHGLLQSV IKRTLGNES VCVGLQKRNY ADNLEFLFAS LGKCFANGLS LNPLACYPPV EFPVPKGTPR LSDMVAGAWD HSAQWLVPKN EDFEGRVQAS GSDSSYSID VSADSPDRYL LDHQVDGREL FPACGCLVLA WKTLAALNGR DFEQMPVRLS RVEIHQAMFL PKSGSATVTV S VMPRTGEF QVCENENLLA SGFVTCPDKD VLETSTHAQT RSSLQDRPAT EVLTRDEVYR ELILRGYEYG PYFQGILRAS VD GQESEIT WDGRWVSFMD SVLQMDILAR PGDYQMLPIK FQSINIDPRV QPAAPAEDED VVVLPGRFDP VLDIVSAGGV EIR GLETIS ASRRLTHAPE VVEEYRFVPH HVTGRDDPGA KRPGATVDIR EYADACLAFA VQGIKKWLSE DKDKVLPQKD LLQD ALGLA NQDLGSKSSS SDFISAKAAL ERILKQQNGH QQHGFGLFHT LNLAFSEPLE IGFRETLKNK IHHMRYDMWD DCLMS AVEC ADSLKLCIDT VAENTTSHIV NVLEAGAAKG AFYRRAIPEA LAKFSGKDYR YTVGDASPMD DAKEFSVKTL QFDAYD PAN FPASQAHAHD LLVLKWVLHQ QEDLDAAMAG FCGFVRPGGF ILVQEFVHRL PTLLAVEAVT DHPLPRKSGD RVLGRYY SA AQWRELFRRH GLVEVIHRSD GALADMFLLR SRVEVMTPPT VLHLDDLSCS WLEEVKAKYS DLEAMPQDAR LWLVGKSD C NGMLGFFNCL RQEPGSERVR CVQVCGDSVP DLSPGSAEFK YLAEMDLAFN VHKDGKWGVY RHLAITDDQR RQQFPTEHA FVDTLTSGDL STLTWVRSPL NLHASSEKGQ DCELCTVYMA GVVSRDLALA CGKLRRDELP AGMFCKEGTL GIEFSGRDTK GKRVMGLCA PPALASSVLC LRSSLWSVPQ HWSLEEAATV PVAYSTAYYA LVIRGHVRPG DTVLVHAGGS PVGQAAIAVA Q SCGCEIFI STATDAETSS LKSMFPRLKD RNFCSCKDAS FERHVKKETS GKGVDIILNC TTGELLGASI RLLASRGRFL NL ASGRGSD AELVFSGSGR RDTSFHDINL DTLIDAQGPE WTELTSLVQK GIQSGLVKPL ARTVYAMDRL VDVFKLLEEG AQA GKLLVK IREEEAEKIT LPAKKTFEAV PRTFFHPAKS YVIVGGLGGF GLELAHWMVL RGVRKLVLTS RNGITTGYQT RKIA FLRSL GADIVVCAVN VTSQAAADRL VKTATDLGPL GGVFNLGLNL RDALLVEQTA ENYKQTLEAK IQTTSLLDGI SRSPK IQPT LDHFVMFSSL SAGHGIPGQT NYGWGNSYMD RLCEKRRAQG LPGLSIQWAS IADVGFVGTK GNNVVIEGKW PQRMYN CLQ VCDYFLSQNR PVVACHVLAE KVKAAVEGEE TVGQQVIKAV GNVLGLKSVS GVDPDKVFLD LGLDSLMSVE IKQMLER DL DLALGTKDIQ MLTFAQLQAM VQHVHHHHHH

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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

Concentration6.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMTris-HCl
100.0 mMNaCl
1.0 mMDTT
0.08 %tween-20

Details: pH measured at 4 degrees C
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 278 K / Instrument: LEICA EM GP / Details: single application, single blot.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.8 mm / Nominal defocus max: 2.2 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: 143694
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 143694
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 34 / Avg.num./class: 4226 / Software - Name: cryoSPARC
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-9cq9:
Modifying region of EcPKS1

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