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- EMDB-16630: The organise full-length structure of the fungal non-reducing pol... -

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Basic information

Entry
Database: EMDB / ID: EMD-16630
TitleThe organise full-length structure of the fungal non-reducing polyketide synthase (NR-PKS) PksA
Map data
Sample
  • Complex: The full-length Non-reducing polyketide synthase PksA
    • Protein or peptide: Norsolorinic acid synthase
KeywordsFungal non-reducing polyketide synthase (NR-PKS) / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


noranthrone synthase / aflatoxin biosynthetic process / norsolorinate anthrone synthase activity / phosphopantetheine binding / identical protein binding
Similarity search - Function
Polyketide product template domain / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / Thioesterase / Thioesterase domain / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain superfamily / Malonyl-CoA ACP transacylase, ACP-binding ...Polyketide product template domain / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / Thioesterase / Thioesterase domain / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain superfamily / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Norsolorinic acid synthase
Similarity search - Component
Biological speciesAspergillus parasiticus (mold)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsMunoz-Hernandez H / Maier T
Funding supportEuropean Union, Switzerland, 2 items
OrganizationGrant numberCountry
European CommissionID: 845941European Union
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: CryoEM structure of the Aspergilus sp. fungal non-reducing polyketide synthase (NR-PKS) PksA at 2.6 Angstroms resolution
Authors: Munoz-Hernandez H / Maier T
History
DepositionFeb 3, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16630.png

Downloads & links

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Map

FileDownload / File: emd_16630.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.25087795 - 0.5293497
Average (Standard dev.)0.0000838613 (±0.014378424)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_16630_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_16630_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 : The full-length Non-reducing polyketide synthase PksA

EntireName: The full-length Non-reducing polyketide synthase PksA
Components
  • Complex: The full-length Non-reducing polyketide synthase PksA
    • Protein or peptide: Norsolorinic acid synthase

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Supramolecule #1: The full-length Non-reducing polyketide synthase PksA

SupramoleculeName: The full-length Non-reducing polyketide synthase PksA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Aspergillus parasiticus (mold)
Molecular weightTheoretical: 450 KDa

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Macromolecule #1: Norsolorinic acid synthase

MacromoleculeName: Norsolorinic acid synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: noranthrone synthase
Source (natural)Organism: Aspergillus parasiticus (mold)
Molecular weightTheoretical: 237.74125 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHHHHHHHH HHGSTSGSGE QKLISEEDLG STSGSGDYKD DDDKLTSLYK KAGLENLYFQ GMAQSRQLFL FGDQTADFVP KLRSLLSVQ DSPILAAFLD QSHYVVRAQM LQSMNTVDHK LARTADLRQM VQKYVDGKLT PAFRTALVCL CQLGCFIREY E ESGNMYPQ ...String:
MAHHHHHHHH HHGSTSGSGE QKLISEEDLG STSGSGDYKD DDDKLTSLYK KAGLENLYFQ GMAQSRQLFL FGDQTADFVP KLRSLLSVQ DSPILAAFLD QSHYVVRAQM LQSMNTVDHK LARTADLRQM VQKYVDGKLT PAFRTALVCL CQLGCFIREY E ESGNMYPQ PSDSYVLGFC MGSLAAVAVS CSRSLSELLP IAVQTVLIAF RLGLCALEMR DRVDGCSDDR GDPWSTIVWG LD PQQARDQ IEVFCRTTNV PQTRRPWISC ISKNAITLSG SPSTLRAFCA MPQMAQHRTA PIPICLPAHN GALFTQADIT TIL DTTPTT PWEQLPGQIP YISHVTGNVV QTSNYRDLIE VALSETLLEQ VRLDLVETGL PRLLQSRQVK SVTIVPFLTR MNET MSNIL PDSFISTETR TDTGRAIPAS GRPGAGKCKL AIVSMSGRFP ESPTTESFWD LLYKGLDVCK EVPRRRWDIN THVDP SGKA RNKGATKWGC WLDFSGDFDP RFFGISPKEA PQMDPAQRMA LMSTYEAMER AGLVPDTTPS TQRDRIGVFH GVTSND WME TNTAQNIDTY FITGGNRGFI PGRINFCFEF AGPSYTNDTA CSSSLAAIHL ACNSLWRGDC DTAVAGGTNM IYTPDGH TG LDKGFFLSRT GNCKPYDDKA DGYCRAEGVG TVFIKRLEDA LADNDPILGV ILDAKTNHSA MSESMTRPHV GAQIDNMT A ALNTTGLHPN DFSYIEMHGT GTQVGDAVEM ESVLSVFAPS ETARKADQPL FVGSAKANVG HGEGVSGVTS LIKVLMMMQ HDTIPPHCGI KPGSKINRNF PDLGARNVHI AFEPKPWPRT HTPRRVLINN FSAAGGNTAL IVEDAPERHW PTEKDPRSSH IVALSAHVG ASMKTNLERL HQYLLKNPHT DLAQLSYTTT ARRWHYLHRV SVTGASVEEV TRKLEMAIQN GDGVSRPKSK P KILFAFTG QGSQYATMGK QVYDAYPSFR EDLEKFDRLA QSHGFPSFLH VCTSPKGDVE EMAPVVVQLA ITCLQMALTN LM TSFGIRP DVTVGHSLGE FAALYAAGVL SASDVVYLVG QRAELLQERC QRGTHAMLAV KATPEALSQW IQDHDCEVAC ING PEDTVL SGTTKNVAEV QRAMTDNGIK CTLLKLPFAF HSAQVQPILD DFEALAQGAT FAKPQLLILS PLLRTEIHEQ GVVT PSYVA QHCRHTVDMA QALRSAREKG LIDDKTLVIE LGPKPLISGM VKMTLGDKIS TLPTLAPNKA IWPSLQKILT SVYTG GWDI NWKKYHAPFA SSQKVVDLPS YGWDLKDYYI PYQGDWCLHR HQQDCKCAAP GHEIKTADYQ VPPESTPHRP SKLDPS KEA FPEIKTTTTL HRVVEETTKP LGATLVVETD ISRKDVNGLA RGHLVDGIPL CTPSFYADIA MQVGQYSMQR LRAGHPG AG AIDGLVDVSD MVVDKALVPH GKGPQLLRTT LTMEWPPKAA ATTRSAKVKF ATYFADGKLD TEHASCTVRF TSDAQLKS L RRSVSEYKTH IRQLHDGHAK GQFMRYNRKT GYKLMSSMAR FNPDYMLLDY LVLNEAENEA ASGVDFSLGS SEGTFAAHP AHVDAITQVA GFAMNANDNV DIEKQVYVNH GWDSFQIYQP LDNSKSYQVY TKMGQAKEND LVHGDVVVLD GEQIVAFFRG LTLRSVPRG ALRVVLQTTV KKADRQLGFK TMPSPPPPTT TMPISPYKPA NTQVSSQAIP AEATHSHTPP QPKHSPVPET A GSAPAAKG VGVSNEKLDA VMRVVSEESG IALEELTDDS NFADMGIDSL SSMVIGSRFR EDLGLDLGPE FSLFIDCTTV RA LKDFMLG SGDAGSGSNV EDPPPSATPG INPETDWSSS ASDSIFASED HGHSSESGAD TGSPPALDLK PYCRPSTSVV LQG LPMVAR KTLFMLPDGG GSAFSYASLP RLKSDTAVVG LNCPYARDPE NMNCTHGAMI ESFCNEIRRR QPRGPYHLGG WSSG GAFAY VVAEALVNQG EEVHSLIIID APIPQAMEQL PRAFYEHCNS IGLFATQPGA SPDGSTEPPS YLIPHFTAVV DVMLD YKLA PLHARRMPKV GIVWAADTVM DERDAPKMKG MHFMIQKRTE FGPDGWDTIM PGASFDIVRA DGANHFTLMQ KEHVSI ISD LIDRVMA

UniProtKB: Norsolorinic acid synthase

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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: 7.8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.2 µm / Calibrated defocus min: 0.9 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Number grids imaged: 1 / Number real images: 6479 / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 468256
Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 361377

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8cg4:
The organise full-length structure of the fungal non-reducing polyketide synthase (NR-PKS) PksA

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