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- EMDB-66475: Cryo-EM structure of PsoA in cofactor bound state (PsoA-PKS-II) -

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Basic information

Entry
Database: EMDB / ID: EMD-66475
TitleCryo-EM structure of PsoA in cofactor bound state (PsoA-PKS-II)
Map data
Sample
  • Complex: PsoA
    • Protein or peptide: PKS-NRPS hybrid synthetase psoA
  • Ligand: COENZYME A
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
KeywordsPKS-NRPS hybrid synthetase / part of the gene cluster that mediates the biosynthesis of pseurotin A / BIOSYNTHETIC PROTEIN
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
PKS-NRPS hybrid synthetase psoA
Similarity search - Component
Biological speciesAspergillus fumigatus (mold) / Aspergillus fumigatus Af293 (mold)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsSun L / Bai L
Funding support China, 1 items
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, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66475.png

Downloads & links

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Map

FileDownload / File: emd_66475.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 576 pix.
= 426.24 Å		0.74 Å/pix.
x 576 pix.
= 426.24 Å		0.74 Å/pix.
x 576 pix.
= 426.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.42574242 - 0.61557007
Average (Standard dev.)-0.00014050078 (±0.014608598)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 426.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66475_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66475_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 : PsoA

EntireName: PsoA
Components
  • Complex: PsoA
    • Protein or peptide: PKS-NRPS hybrid synthetase psoA
  • Ligand: COENZYME A
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Supramolecule #1: PsoA

SupramoleculeName: PsoA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Aspergillus fumigatus (mold)

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Macromolecule #1: PKS-NRPS hybrid synthetase psoA

MacromoleculeName: PKS-NRPS hybrid synthetase psoA / 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: Aspergillus fumigatus Af293 (mold)
Molecular weightTheoretical: 436.200625 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MVYTHSPKEP IAIIGTGCRF PGGSTSPSKL WDLLYSPRDL TREVPAESRF NPKGFYNVDG EHHGASNATN AYFIEEDPRY FDAGFFSIA PREAESIDPQ QRLLLETVYE AMENAGLTLN GMRGSATSAY MGAMSADYTD TQLRDIENVS KYMITGTSRA L LANRLSYF ...String:
MVYTHSPKEP IAIIGTGCRF PGGSTSPSKL WDLLYSPRDL TREVPAESRF NPKGFYNVDG EHHGASNATN AYFIEEDPRY FDAGFFSIA PREAESIDPQ QRLLLETVYE AMENAGLTLN GMRGSATSAY MGAMSADYTD TQLRDIENVS KYMITGTSRA L LANRLSYF FDWKGPSISV DTACSSSLAA VHLGVQALRA GECTISCVGG SNIILNPDCY LAATSLHLLS PTGRSQMWDQ AA DGYARGE GVCVFFMKTL SQALRDGDRI DALLRETCVN SDGRTQGIAL PSAEAQVSLM RTAYKNAGLD LSKAEDRPQY IEA HGTGTQ AGDPREAYAI ATTFFPPGED HSHRPKLVVG SVKTIIGHTE GCAGIAGILK AVLAMRHKTI PPNQHFHNLN PSVK PSFKH LSIATSPQPW PVVPPDTPLR ASVNGFGSGG TNCHAIVESY VPEIHDNGPW GKPKEMTQVP NGVAAPETDF SPIPL IFSA SSGTALRAML ERYQEYLERT EVSLLRLAMT LNSHRSTLPV RVSIPGTSKA DVLAAIRTQL AKVGSNPGAE IGTRSS VPE FDHVRRPKIL GVFTGQGAQW AGMGQGLMAK SALFRQVIEV MEEAMAQLPD GPEWSLKEEI MKPPKTSRLG EAEISLP VC AALQVGLVKV LRSAGITFSM VVGHSGGEIG SAYAAGKISE VDAIKIAYYR GVYTKLAIGK DGKKGGMIAV GFGYEDGL N FCAMEQFADR LTVAASNSPK SVTLSGDLDA VHEAKELLDA EGVFNRVLRL DTAYHSPHMY PCAAPYLAAI ERCGLVAGK SNGTAWASSV YDDNRMMTSA QDKDLEAAYW KDNLIGRVLF SQAVERALDE GNGDFDLALE IGPHPSLKGP TLETIRHKIG SEIPYSGVL DRKADDILAL STALGFSWLT LGSGVVDFAG YVSGFDPSNA SILNAPALPD LPTYPWDHKK VLYRESRLNK N VRHRVDPP HPLLGSRTPD DTDYEPRWRN FLIMEELPWL RDHCVQGQII VPAATYSVMA LEAAKVLCRG KHVQSIELSD VA ILRPIVL DEASDGTETL FSVRSDLDSN KKHEDEIHAQ FTLSAGAMDD RHLRTAATGH IRITLAAEAP SSFPNGPRPT ELD LLPTSV DRFYASMDEI GLSYSGPFRA MTSMKRRLNV ASATVAVDRD LAGTIPVHPT WLDACFQTFL AAFAAPRDGS LWTA FMPTA IGRMVFSPSS TSQVPGRSVT VDAHITDFAP GYQVSLPTLT GDMSIFNSET NQLQIQIEDF VMSSFLPASE KDDRR FYLQ NVWGQEMLSG ALCAAAERCV APTESESKII DTCEKAVHYY LSKLKAAGLL DQWADKNPGL RSLMNEIEAR VTSIPE QSD LVSMLGEVGE HIDLVLVRTI GESLLNSPSE GLGPITPSPM GALISRWHHE GLGFAQLQRH FVSAAKQISH QHANLRI LQ VGPSSPGLVR SVCQELGRSL ERYTLVDDSE QTIEEMKSAL AADQLRVDFT TASVENGIDA VNHLTSAGGF DLVIVHKA F TKQVTALKTV RNLLRPGGFM LMMAATGAQL RFPFMLMSTL PSLDDERLAQ TKFINATRAE THDLLRQIGF SGVDSIALD NVPDKHTFSV VVSQALDDHI AFLRSPLTSP SPVPLSGNLL VVGGFSADIA KLATAIQSLV STVWHGDIIN VRTLAELDDE ASTVEAVLS LTDLDRPVLE DVRAPTFRGL QRLFSEAKTV LWITHRAKAD NPYHNATIGL GRSFQSENPQ KVLQFLDVDT L DGVESAIA ETFLKLIGGV NMRNSNPADP TRLWTIEPEV SLENGKYLVP RLFPDTERND RLNALRRKVQ TQVSVETQPI SL SRSAQSD QVAYTAEAVH FHRDLADGAT DPVTIQVELC STEPVIPNID NEDLFCFVGR TSEGARLVGL STSNSSVVKV PRE WTIPVD KHTSHDQGAF VLELRNEIQS LVIAKSIPPG STTLIYEPDP HLAASLQRPG RPATSSVSFR ARSTWSIPGS HILI DPHAS RKDIQAKVPP KTRMLIHMEQ GPETCEFLAL RQALPPYATV VAFNDLAADD VNPRELLAEA LSIIRGDSQS TKVPF DPSS VVKASALVAG GTREHANAAV VDWTGAQSIT LSPRPVDTRN LFSPNKTYLL VGLTGHIGQS ICRWMVQGGA RHIVVT SRH PEKQGQLWRE ELLRQGVNIV IEAADVTKEH DLLDLRARIV SSMPPVGGIA NGAMVLDDKL FIDMPFESFQ AAMKPKV QG SIYLEEVFSA DNLDFFLFFS SISVMTGQRT QANYVAANNF MVAMAERRRA RGLPASVIDI GMVVGIGVIQ RSQNDKGV S AMENSIRQMD YMPVSETDLH HLLAEAILVG QRDESPELIT GLETYKPVEG EAPFWHHNVR FSHLITDPDA AQAGADSAG SAQKSLKEML LSSGGPEEAR KVMENALLQY LASSLKLSRE TIYTDVPIID LGIDSLVAVQ IRNWTWAEAG YDLPVLKILG GSSVTQICD EVVASLSFDK SSIAAAKVDS QAAPAHKLRP WDKPSADTKR TDSIAPVPRS QIAANGPNGL PNGALKKASK L AVKVRPLW TTQAGGKDTK KGPRPAPIRI QPLSLGQSRL YFLSQYMDDD RVLNCTISYA LSGKLDVSKL EQSLIQVVQR HE ALRTSFY TDEKDGKPMQ GLLEKSPFRL RVVPGVSASS DVETEFNLIR YRPYDLEQAD TFAATLLSHS PDSHTLICGY HHI IMDGVS WQIFQKDLAM FYNNSGIADS AKHLPAQYSE FTRKQQEDLS CGAYAERLRF FQDQFREPVE SLPLFPFAKV GTRK VVKQY AVQEATTHLN AKVVSAIKQA SQTSRTTPFH FYLSAFQVLL HRLLETDKMC IGVVDANRSD QNFVNTIGFF LETIP LWFK VNSEQRFVEL LKETRTKAYA ALAQTGVPTE EILRACGVAS STTETPLFQV CFNYRMGAGR TAALQGVEMK FLDYVD AQN PFDLVATVDD LDDGTAMITL YLQDYLYDQE GAQLLATMYA NVLQVLAENP ERLVGSVSIS NATLEDEGVK LGTGPIL DL VAPSTPTLSK IFHTWVDKDP HALAVKDTTG KSKTYVQLAE RANAIAASLL NAGAAPSIPI GVLLDPGVDT IATILAIL R IGAAYVPLDT RSSDAVLSDI LQESQPGIVI HHSATAPRSQ ILLKASAKTK LVTLNAVPQK TIRKIQDVSV PEGLAMILY TSGSTGSPKG IPLTNANIRT PILGVSERVP LGREVVLQQS GQGFDAAVYQ IFIALANGGT LIMVDNRDDP AKVAALMAQE SVTCTTHIV SEMQALLKYG YDELRNCSSW RIAMVAGEAF TVHLLDQFRA LNRPDLKVIN AYGPTEASIC SSLGEVSFNR I SSSETSIP IGKAIPNYGT YIVDQHCKPV PLGWPGEVAI AGPGVASGYL NLGELTQAKF RSAATLGEVF GSDCLYLTGD RG RMLSDGS IVLSGRVDGD DQVKIRGHRV QLGDVARALV QASRGVFADA AVILKGDDTS NPQLVAYVVF SRTSNIQDQQ TYL RQLNQD LPVPAYMRPA ITIPLDTLPV TDRGKLDSKK LASLPLPSIS VDYEEDEQLT PTEARLRDVW KNVLGDIASS IPIR RSSDF FSVGGNSLIL LALKAEIAQV FGVGLSVSEL FQASTLELLA ARLDGTSLLA QINWEEETAP DETQFTLPPP INGIN GHGS SNGHAQGISV LLTGATGFLG GHILRQLVQL PSVEHVHCVA IRPNKVDVRR QLSVESPKII RYSGDLALPN MGMSES EFS DLFKSIDVIV HNGAEVSHMK NYRSLRAANF LSTVGLARAA VSRGIPIHYI STGGVARLSV ADEQPEASLA AFHPPID GS DGYVASKWAS EVFLEKVQRR FQGQVWIHRP SSITGDDVPD NDIAHSLLKF SRELGAVPEL TGSGFFDFIN VETVSNNI A ASVVRSSEKS GGGLIYLHQS GEQVIPVGDL QKYVEELEGR PLQVLPLKEW VDLSIRKGLD EVLGSYMLAS KGVIRAPLL QRGPHVE

UniProtKB: PKS-NRPS hybrid synthetase psoA

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Macromolecule #2: COENZYME A

MacromoleculeName: COENZYME A / type: ligand / ID: 2 / Number of copies: 2 / Formula: COZ
Molecular weightTheoretical: 767.534 Da
Chemical component information

ChemComp-COA:
COENZYME A

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Macromolecule #3: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 3 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.4 / Component - Concentration: 0.15 M / Component - Formula: NaCl / Component - Name: sodium chloride
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 107200
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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