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- PDB-9nju: Structure of native homodimer of D. discoideum polyketide synthas... -

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Entry
Database: PDB / ID: 9nju
TitleStructure of native homodimer of D. discoideum polyketide synthase Pks16
ComponentsProbable polyketide synthase 16
KeywordsTRANSFERASE / fatty acid synthase activity
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsHoogerbrugge, G. / Keatinge-Clay, A.T. / Marcotte, E.M.
Funding support United States, 5items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
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Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Mar 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 2.0Jan 7, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
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Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update / _entity_src_nat.common_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.details / _pdbx_struct_oper_list.symmetry_operation / _refine_ls_restr.dev_ideal / _refine_ls_restr.number
Description: Atoms with unrealistic or zero occupancies
Details: I removed a residue that had zero occupancy, and I changed peptides that were identified to be in the cis- conformation to the trans- conformation.
Provider: author / Type: Coordinate replacement
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Item: _citation.journal_volume / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable polyketide synthase 16
B: Probable polyketide synthase 16


Theoretical massNumber of molelcules
Total (without water)582,4142
Polymers582,4142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Probable polyketide synthase 16 / dipks16


Mass: 291206.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum AX2 (eukaryote)
References: UniProt: Q869W9, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homodimer assembly of polyketide synthase Pks16 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Dictyostelium discoideum AX2 (eukaryote)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 49 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5particle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC4.53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5611 / Symmetry type: POINT
RefinementHighest resolution: 3.94 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00238234
ELECTRON MICROSCOPYf_angle_d0.53451700
ELECTRON MICROSCOPYf_dihedral_angle_d7.1995174
ELECTRON MICROSCOPYf_chiral_restr0.0425880
ELECTRON MICROSCOPYf_plane_restr0.0036616

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