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- PDB-9x2a: Cryo-EM structure of PsoA in cofactor bound state (PsoA-PKS-II) -

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Basic information

Entry
Database: PDB / ID: 9x2a
TitleCryo-EM structure of PsoA in cofactor bound state (PsoA-PKS-II)
ComponentsPKS-NRPS hybrid synthetase psoA
KeywordsBIOSYNTHETIC PROTEIN / PKS-NRPS hybrid synthetase / part of the gene cluster that mediates the biosynthesis of pseurotin A
Function / homology
Function and homology information


pseurotin A biosynthetic process / nonribosomal peptide biosynthetic process / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / secondary metabolic process / secondary metabolite biosynthetic process / fatty acid synthase activity / ligase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process
Similarity search - Function
Highly reducing polyketide synthase sdgA, C-terminal ACP domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / : / RhiE-like, KS-MAT linker domain / : / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Polyketide synthase, dehydratase domain ...Highly reducing polyketide synthase sdgA, C-terminal ACP domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / : / RhiE-like, KS-MAT linker domain / : / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / ANL, N-terminal domain / : / AMP-binding, conserved site / Putative AMP-binding domain signature. / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Chloramphenicol acetyltransferase-like domain superfamily / : / Acyl transferase/acyl hydrolase/lysophospholipase / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / AMP-binding enzyme, C-terminal domain superfamily / 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 / Short-chain dehydrogenases/reductases family signature. / Thiolase-like / Phosphopantetheine attachment site / 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
COENZYME A / Chem-NDP / PKS-NRPS hybrid synthetase psoA
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsSun, L. / Bai, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171212 China
CitationJournal: To Be Published
Title: Mechanistic insights into the biosynthesis of Pseurotin A in Aspergillus fumigatus
Authors: Sun, L. / Bai, L.
History
DepositionOct 4, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PKS-NRPS hybrid synthetase psoA
B: PKS-NRPS hybrid synthetase psoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)875,4276
Polymers872,4012
Non-polymers3,0264
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 PKS-NRPS hybrid synthetase psoA / Nonribosomal peptide synthetase 14 / NRPS14 / Pseurotin biosynthesis protein A


Mass: 436200.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: NRPS14, pesO, AFUA_8G00540 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BY4742
References: UniProt: Q4WAZ9, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-COZ / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: PsoA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Aspergillus fumigatus (mold)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BY4742
Buffer solutionpH: 7.4
Buffer componentConc.: 0.15 M / Name: sodium chloride / Formula: NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.1_5286model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107200 / Symmetry type: POINT
RefinementHighest resolution: 3.36 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00237460
ELECTRON MICROSCOPYf_angle_d0.50750972
ELECTRON MICROSCOPYf_dihedral_angle_d6.6375285
ELECTRON MICROSCOPYf_chiral_restr0.0415780
ELECTRON MICROSCOPYf_plane_restr0.0046670

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