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- EMDB-49491: Structure of native homodimer of D. discoideum polyketide synthas... -

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Basic information

Entry
Database: EMDB / ID: EMD-49491
TitleStructure of native homodimer of D. discoideum polyketide synthase Pks16
Map data
Sample
  • Complex: Homodimer assembly of polyketide synthase Pks16
    • Protein or peptide: Probable polyketide synthase 16
Keywordsfatty acid synthase activity / TRANSFERASE
Function / homology
Function and homology information


Vitamin B5 (pantothenate) metabolism / Fatty acyl-CoA biosynthesis / sexual reproduction / fatty acid synthase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / oxidoreductase activity
Similarity search - Function
Highly reducing polyketide synthase sdgA, C-terminal ACP domain / : / Anamorsin, N-terminal / : / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / : / Polyketide synthase dehydratase domain / : ...Highly reducing polyketide synthase sdgA, C-terminal ACP domain / : / Anamorsin, N-terminal / : / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Acyl transferase domain superfamily / Polyketide synthase, enoylreductase domain / Enoylreductase / Acyl transferase/acyl hydrolase/lysophospholipase / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / GroES-like superfamily / Thiolase-like / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Probable polyketide synthase 16
Similarity search - Component
Biological speciesDictyostelium discoideum AX2 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsHoogerbrugge G / Keatinge-Clay AT / Marcotte EM
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM106112 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM122480 United States
Department of Defense (DOD, United States)W911NF-12-1-0390 United States
Welch FoundationF-1712 United States
Welch FoundationF-1515 United States
CitationJournal: Mol Cell Proteomics / Year: 2026
Title: Serendipity and the Slime Mold: A Visual Survey of High-Molecular-Weight Protein Assemblies Reveals the Structure of the Polyketide Synthase Pks16.
Authors: Gabriel Hoogerbrugge / Adrian T Keatinge-Clay / Edward M Marcotte /
Abstract: Large macromolecular assemblies are integral to most cellular processes, making their identification and structural characterization an important strategy for advancing our understanding of protein ...Large macromolecular assemblies are integral to most cellular processes, making their identification and structural characterization an important strategy for advancing our understanding of protein functions. In this pilot study, we investigated large multiprotein assemblies from the cytoplasm of the slime mold Dictyostelium discoideum using shotgun electron microscopy, the combined application of mass spectrometry-based proteomics and cryo-EM to heterogenous mixtures of proteins. With its similarities in cell structure and behavior to mammalian cells, D. discoideum has long served as an invaluable model organism, particularly in the study of immune cell chemotaxis, phagocytosis, bacterial infection, and other processes. We subjected D. discoideum soluble protein complexes to two-step fractionation, performing size-exclusion chromatography followed by mixed-bed ion-exchange chromatography. Isolated fractions containing a subset of high molecular weight-scale protein assemblies were subsequently analyzed using mass spectrometry to identify the proteins and cryo-EM to characterize their structures. Mass spectrometry analysis revealed 179 unique proteins in the isolated fractions, then single-particle cryo-EM analysis generated distinct 2D projections of several visually distinctive protein assemblies, from which we successfully identified and reconstructed three major protein complexes: the 20S proteasome, the dihydrolipoyllysine-residue succinyltransferase (Odo2) of the mitochondrial 2-oxoglutarate dehydrogenase complex, and polyketide synthase 16 (Pks16), thought to be the primary fatty acid synthase of D. discoideum. Based on the Pks16 structure, the first of the 40 D. discoideum PKSs to be experimentally determined, models for the full set of D. discoideum PKSs were constructed with help from AlphaFold 3. Comparative analysis enabled structural characterization of their reaction chambers. Shotgun EM thus provides a view of proteins in their native or near-native biological conformations and scaling up this approach offers an effective route to characterize new structures of multiprotein assemblies directly from complex samples.
History
DepositionFeb 27, 2025-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49491.png

Downloads & links

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Map

FileDownload / File: emd_49491.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.)
1.75 Å/pix.
x 256 pix.
= 447.846 Å		1.75 Å/pix.
x 256 pix.
= 447.846 Å		1.75 Å/pix.
x 256 pix.
= 447.846 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7494 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.239
Minimum - Maximum-0.7127824 - 1.4440316
Average (Standard dev.)0.000146439 (±0.04827559)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 447.8464 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49491_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49491_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49491_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homodimer assembly of polyketide synthase Pks16

EntireName: Homodimer assembly of polyketide synthase Pks16
Components
  • Complex: Homodimer assembly of polyketide synthase Pks16
    • Protein or peptide: Probable polyketide synthase 16

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Supramolecule #1: Homodimer assembly of polyketide synthase Pks16

SupramoleculeName: Homodimer assembly of polyketide synthase Pks16 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Dictyostelium discoideum AX2 (eukaryote)

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Macromolecule #1: Probable polyketide synthase 16

MacromoleculeName: Probable polyketide synthase 16 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Source (natural)Organism: Dictyostelium discoideum AX2 (eukaryote)
Molecular weightTheoretical: 291.20675 KDa
SequenceString: MTFNNIKDEN NDDIAIIGMG FRFPGGGNNP DQFWNQLSNK MDGISKISQE KWSRSFYEQK YINNEYGGVL KDEEWKNFDP LFFGISPKE APTIDPQQRL LMTTLWEAFE DANIKPSTLR GSDTAVFIGM MNLDYQRCQF RDISYINPYT VTGSAGSFVS N RLSFSFDL ...String:
MTFNNIKDEN NDDIAIIGMG FRFPGGGNNP DQFWNQLSNK MDGISKISQE KWSRSFYEQK YINNEYGGVL KDEEWKNFDP LFFGISPKE APTIDPQQRL LMTTLWEAFE DANIKPSTLR GSDTAVFIGM MNLDYQRCQF RDISYINPYT VTGSAGSFVS N RLSFSFDL RGPSMTLDTA CSSSLNAVYL GCQAIATGDS KMAIVGGVNG IFDPSISMTF SGLNMLGHKG QCRSFDAGAD GY IRSEGGG VCILKKYSDA IKDGDRIYCV IKGGSSNVDG YNAKTNITQP SMKAQGENIE IALKKSGVNP SDIYYIEAHG TGT PVGDPI EIEAISRIFK DNHTPDAPLY IGSVKSNIGH LESAAGIASL IKVALSLKNR SLVPNIHFEK PNPLIKFEDW NIRV VTDEI QFPTNKLINM GINCFGLSGS NCHMILSEAP INYDELLKTT NNNSTSSSSN DDKKEYLIPF SANCNISLDK YIEKL ISNQ SIYKDTILFK DFVKHQTISK SNLIKRKVIT ASDWDDFLNK RNETTSTSSL TSTISAPASS TPVIYVFTGQ GPQWRD MGK ALYETESVFK DAIDHCDKLL ANYFGYSILQ KLRSLESDDS PEIHHPILAQ PSIFLIQVGL VALYKSFGIS PSIVVGH SF GEVSSALFSG VISLETAVKI VYYRGLAQNL TMGTGRLLSI GIGADAYLEK CALLYPEIEI ACYNDPNSIV ITGSEQDL L GAKSTLSAEG VFCAFLGTPC SFHSSKQEMI KEKIFKDLSD LPESNVPCVP FFSTITGSQL SHKGFYNVQY IYDNLRMPV EFTKAISNIF NFIEENESYK NAIFLEIGPH PTLGFYIPKC KPSNSTITSK PIIVSPLHKK KEELTQFKLA ISTLYCNGVE IDFASGQQL LPTSSSSGGG DISSFKESTN KLPRYQWDFE EYWDEPNQSK MVKRGPSNNL LGHDQFAGNT LMELFIDINK S AHQYLKGH KIKGKYLFPG SGYIDNILRQ FNGQDITIFN LEFSNPFFLK DGVQHHLQTS ITPTTKGEFK VEFFIKDNRN ST KWTKTSN GRIGLFKHNP KNNKLDIEKL KSQCSFTTLT KSEVYNKLLL LSLPYGPTFQ RVESCSIGDG CSFFKLSMSP CSE FDKDFL NPSIIDCAFH GLLVLSEGPQ EIVFDRLQDM KFYSSNVPST RPQFIYAFAK FDKIVGNSTH GSLDIMLEDG TLLI SIKNV KCTSLIRLKK QSIKYPSQNV YSHHWQSKDS PLTLIENQLI EEKSSESKIN FEKLLNDKLF NDYLIRLLNQ SIKSE FIEF DYKTSTVDTL EIDSNNTKLL EKIQSILKTI DSLDQSIDLA SLKQVIIEKS SSFKKEINLI EKSIKRIVSL LKGGES EHF SPSNPSSPND TPRYNSNNCS SKSNNTSSGA DDDTNNEETI NQLNNEPFNF SNSQFISNQN QLISKTIVNS FDRLINS IE IGEKKLIKII DLSSIYQNNQ LSKLLLLQLN QLLINLSNNN NIEIEYTIPS NTKNIDSIKE ETKSISNLLN IKYRSFDL Q DDLESNGYLN SNYDLIITSL LLVSTNSIDS NEVLSKLYKL LLPKGQLILM EPPKDVLSFN LLFANDFKQS LEIKSEQEI KSLIRYCGFT KIETNNITQD DEEEQQQPPS ILIVQTEKRD IESMSLTFSS DPESLNSSYS NCIFIVSKEQ KENPTSYIQE YFDITEVFC DNTTIIEAGD SELLTKTIES GIGKNDIIFF LVSLEELTIE NYKQVTMQYT LVNQILLRNN LSTRFALLTY D SQNGGKNY LGSSLIGTFR YFLEFPSLNT FSIDVDKDSI DNLTLFLRLV DLSTIGDRET IVRNNKIFVQ KIFKEPKLLS PS NNYEKDT NNLYLNTNSN LDFSFQCKEK LPHGSVEIKV MSTGINYKDN LFYRGLLPQE IFTKGDIYSP PFGLECAGYI TRV APSGVT RFKVGDQVVG FASHSLSSLA ITHQDKIVLK PENISFNEAA AVCVVYATSY YSIFHIGAFM ADKESILVHS ATGG VGLAT LNLLKWKRNQ LKKHGNSEIS NDASIYATVG SKEKVDYLQE KYGDLITAIY NSRDTEYCDE IKQQSAQGGV DLILN TLSG DYLSANFRSL SQVGRIMDLS VTQLVENDSL DFSNFKYHVT YSTIDLERAT TYNSKIVRDI LTEVFDAISD GSLENI PVK VFPATQVKTA IEYINERVHI GKIVVDFENF EQDILKPALQ EKENPIQLNK VKKLEHTCDT LNNTILITGQ TGIAVHI LK WIISGSVLNS NKSQQQVTDF IILSRSSLKW ELENLINQTK HKYGDRFRFH YKSVNIADLN STRTAIDQVY SSCKNVSP I KSVLHFATVY EYILPEDITQ TVIDNTHNPK AVGAINLHNL SIEKDWKLEN FILFSSIGAI IGGSKQCAYS SANLVLDSL SNYRKSIGLA STSINWGGLD AGGVAATDKS VASFLEGQGI LLVSLSKILG CLDSVFQPSN SHLSNFMLSS FNIDNLLSSA PQMKRKMGH HLTNYKTSSA SSDDSLGDSS STQAKVISTI SELLSIHPSK LNLDTRLKDY GIDSLLTVQL KNWIDKEFTK N LFTHLQLS SSSINSIIQR ISSKSTSTST PNPTNTTKQT ATTKT

UniProtKB: Probable polyketide synthase 16

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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

BufferpH: 7.4
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 5611
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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