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- EMDB-45913: Full length EcPKS2 - acylated dataset with three ACP positions -

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Basic information

Entry
Database: EMDB / ID: EMD-45913
TitleFull length EcPKS2 - acylated dataset with three ACP positions
Map dataUnsharpened map for FL EcPKS2 - acylated dataset
Sample
  • Complex: Homodimer of EcPKS2
    • Protein or peptide: Polyketide synthase 2
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] ethanethioate
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: 3.1 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 25, 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_45913.png

Downloads & links

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Map

FileDownload / File: emd_45913.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map for FL EcPKS2 - acylated dataset
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0704
Minimum - Maximum-0.2814992 - 0.7791006
Average (Standard dev.)0.0025050011 (±0.026270244)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45913_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B

Fileemd_45913_half_map_1.map
AnnotationHalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half A

Fileemd_45913_half_map_2.map
AnnotationHalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Homodimer of EcPKS2

EntireName: Homodimer of EcPKS2
Components
  • Complex: Homodimer of EcPKS2
    • Protein or peptide: Polyketide synthase 2
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] ethanethioate

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Supramolecule #1: Homodimer of EcPKS2

SupramoleculeName: Homodimer of EcPKS2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Elysia chlorotica (eastern emerald elysia)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Polyketide synthase 2

MacromoleculeName: Polyketide synthase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Elysia chlorotica (eastern emerald elysia)
Molecular weightTheoretical: 253.035688 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MAPQEQASSS QQDDAPPKTP NVVEPYKGEV AICGLSGRYP ESANVGELEY NLFNKIDMVT IDNRRWEPGY LGTPERMGKV KTITDFDAE FFGVHTKGAQ TMDPMLRNLL EVVYEAIVDA GESLESMKGT RTGVYIGVSN NEVDTAYMKN WTDDDAYMVQ G CHHSMYPN ...String:
MAPQEQASSS QQDDAPPKTP NVVEPYKGEV AICGLSGRYP ESANVGELEY NLFNKIDMVT IDNRRWEPGY LGTPERMGKV KTITDFDAE FFGVHTKGAQ TMDPMLRNLL EVVYEAIVDA GESLESMKGT RTGVYIGVSN NEVDTAYMKN WTDDDAYMVQ G CHHSMYPN WISFFFDFSG PSTAYNTA(SCY)S TSLVCLDAAE RHLRMGVIDN AIVGGSNFIY RPATTKLFMG MNFLGSST C KAFDESGDGF VRGEVASAIL LKKADTAKRV YCTLVGSMLN NDGNQTNGIL YPNSEAQEQL MTDIYSTHKI DANEVKYFE CHGTGTQAGD PNETRAICNA VCKGKKDPLL IGSIKSNLGH GETASGINGI SKVIITMHSR QIPPNLHFKN PNPKIPGLFD GRLKVVTET TPFDGGLIAI NSFGMGGTNA HAIFRSFDKR AEPHPASDKP RLFTYCARTE EGLQKIFEEA HKHASNVEFH A LCQESANT KPKSLPYRGA TILNAEGEYT EIQKCPSKAR EVWFVYSGMG SQWVGMGRSL MALDVFRQSI EETAAILSPF GV DLMSLLM DGTEDKLKEI MPPFICINAI QLALTDLLNS MGIVPDGLVG HSLGEVGCAY ADGCLTRREA ILSAFWRAKA VID CEVKPG KMAAVELTWE EAKRLCPPGV VAACHNSQDS VTISGGAQEM TKFMAELSAQ GVTVKEVNSN NISYHSSFMT EPAA YLKKG LEKEIVPKPR SKKWISTSIP EERWGNPEAQ TADASYQANN LLSSVLFYEG LQKIPSNAIA IEIAPAGLLQ SVIKK SLGQ DCTIVALQKR KSPNNLEVFF SALGKCYSHG VPMNPLGLYP AVQFPVSIDT PMLSSMVSEA WDHSAKWRVP LVEEFE YGS GSSSDNVIDI DLSEDSPENY LLEHAVDGRM LFPATGTLVL AWKTLAKLKG VEFEQLGVQM TNVQIHQALF LNPGGKT TV SVSVMPITGE FQVRDGESLI SSGVITSSEG RLLETDQHMK KGSVLDGKPD KELLFTKEIY REFLLRGYEY GAAFQGIQ R ASLDATDTDI RWDGRWISYL DTVLQMYLLS KPGTHQALPT LLESVTIDPR VHPAQPPEGT TEFQVLPGKW DPVLQIAAA GGVEIRSCHS IRASRRLNHD PPILEDFAFA PYVDPRPSDR SAAAVTPALR DYADACFEFS RQGMKRWLEN DKNNVLPNKE EIKEALAMA NKHASTPQAA SNFASAKATL EALVNNKNGH RLPNHGLFEM LDIAFSEPLE GDYWDRLRMK LHDVRTYLWD D PIIAALES PDIVKLVMET VSDNVNQQVM EILEVGAARG PYYRQAIPKA LEYFSIKDWQ YTVADQGFVE DAAEFPVKMM QF DPLDPAN FPAELTESCD LLVLKWNLQM QVDLDAAITE FSKMIKPGGF LLVLENGTRL STFFPIKAIV SASLGGKGGP EGD RAMGCF YTDAQWSALF ARHGFEQIMH IPDGIAVSMF LLRKPFEPSV APIIINVDDL ECSWLEEVQA RCAELQDSHK DSRL WLVAN TELSGVLGFL RSLVWEFGSE KLRCIQIDDA TAGPNPPKIS ADSADFKELV RKDLAYNVFK NGKWGTYRGF VISDA DRQK ERPSEYVYAD WLSAGDMSSL RWFDSPLKTG HNNGMLGSKM AHKLETETCS VYYAGLNLRD IILANGTIQR DILPEE TFF KEGVLGVEFS GRNSSGKRVM GLCPPPALAT TVKCPVSSLW SVPDQWTLEE AATVPLAYAT AYYCLVSEGG VQKGATV FI HAGASVVGQA SIAVALSYNC EIFTLTKNSD ETALLKSMYP QLNDRNFCSS EDCSFEKYIR KETKGSGVDV VINTLRGK F LKASRRLLSK KGKFVDIGFK VDSNTQIAYY TREHPDLRFQ LDALLESQGP EWTRLFDLVQ AGIHSGVVKP LKRAVYSMD KIVDAFKTVE AEREAGKIVI KIRDEERQKV CPTPRTSFPA IHRTCFHPDK SHILVGGMGG MGLETAHWMV LRGAKKLILT SRYGITTGY QARKIAFFKQ LGVEVEVLAL SVNTRKAADK VFEHALKMGP VGGIFNMAMV LYNDDFLKMN REQFLKPLES K ITMTMLLD DKSREKPVRD TLDHFVMFSS LIVSGGHLGQ ANYAFGSTVL EKICERRKRD GLPVTTPQWA SIADVGTVAL MG TGNETII CRKYPQRFFN VLSVFDFMMS SDNVVTISYV LVEKSMGVAA GEESMVDQVL RAVGKVLGIK DVSSVDGDKE FID MGVDSL MSVEIKQALE RDAGLVISTK DTQLMTFNTL RSMVKGSHVH HHHHH

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Macromolecule #2: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 2 / Number of copies: 2 / Formula: NDP
Molecular weightTheoretical: 745.421 Da
Chemical component information

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Macromolecule #3: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...

MacromoleculeName: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] ethanethioate
type: ligand / ID: 3 / Number of copies: 2 / Formula: 6VG
Molecular weightTheoretical: 400.385 Da
Chemical component information

ChemComp-6VG:
~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] ethanethioate

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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 K3 (6k 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: 614919
Startup modelType of model: NONE
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 168733
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationSoftware - 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-9cto:
Full length EcPKS2 - acylated dataset with three ACP positions

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