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Yorodumi- EMDB-12139: Fatty acid synthase (FAS) from Pichia pastoris, including ACP dom... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12139 | ||||||||||||
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Title | Fatty acid synthase (FAS) from Pichia pastoris, including ACP domain resolved by focussed classification | ||||||||||||
Map data | Sharpened map. Derived from focussed classification of ACP domain containing region. | ||||||||||||
Sample |
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Keywords | Multienzyme / Complex / Fatty acid / Synthase / BIOSYNTHETIC PROTEIN | ||||||||||||
Function / homology | Function and homology information mitotic nuclear membrane biogenesis / palmitic acid biosynthetic process / fatty-acyl-CoA synthase system / fatty-acyl-CoA synthase activity / fatty acid synthase complex / holo-[acyl-carrier-protein] synthase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid synthase activity ...mitotic nuclear membrane biogenesis / palmitic acid biosynthetic process / fatty-acyl-CoA synthase system / fatty-acyl-CoA synthase activity / fatty acid synthase complex / holo-[acyl-carrier-protein] synthase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid synthase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / magnesium ion binding Similarity search - Function | ||||||||||||
Biological species | Komagataella phaffii GS115 (fungus) / Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Snowden JS / Alzahrani J | ||||||||||||
Funding support | United Kingdom, Saudi Arabia, 3 items
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Citation | Journal: Sci Rep / Year: 2021 Title: Structural insight into Pichia pastoris fatty acid synthase. Authors: Joseph S Snowden / Jehad Alzahrani / Lee Sherry / Martin Stacey / David J Rowlands / Neil A Ranson / Nicola J Stonehouse / Abstract: Type I fatty acid synthases (FASs) are critical metabolic enzymes which are common targets for bioengineering in the production of biofuels and other products. Serendipitously, we identified FAS as a ...Type I fatty acid synthases (FASs) are critical metabolic enzymes which are common targets for bioengineering in the production of biofuels and other products. Serendipitously, we identified FAS as a contaminant in a cryoEM dataset of virus-like particles (VLPs) purified from P. pastoris, an important model organism and common expression system used in protein production. From these data, we determined the structure of P. pastoris FAS to 3.1 Å resolution. While the overall organisation of the complex was typical of type I FASs, we identified several differences in both structural and enzymatic domains through comparison with the prototypical yeast FAS from S. cerevisiae. Using focussed classification, we were also able to resolve and model the mobile acyl-carrier protein (ACP) domain, which is key for function. Ultimately, the structure reported here will be a useful resource for further efforts to engineer yeast FAS for synthesis of alternate products. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12139.map.gz | 348.3 MB | EMDB map data format | |
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Header (meta data) | emd-12139-v30.xml emd-12139.xml | 22.6 KB 22.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12139_fsc.xml | 16.3 KB | Display | FSC data file |
Images | emd_12139.png | 198.7 KB | ||
Masks | emd_12139_msk_1.map | 371.3 MB | Mask map | |
Filedesc metadata | emd-12139.cif.gz | 7 KB | ||
Others | emd_12139_additional_1.map.gz emd_12139_additional_2.map.gz emd_12139_half_map_1.map.gz emd_12139_half_map_2.map.gz | 41.3 MB 397 KB 297.3 MB 297.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12139 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12139 | HTTPS FTP |
-Related structure data
Related structure data | 7bc5MC 7bc4C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12139.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map. Derived from focussed classification of ACP domain containing region. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12139_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Sharpened map with solvent mask applied.
File | emd_12139_additional_1.map | ||||||||||||
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Annotation | Sharpened map with solvent mask applied. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focussed mask used for focussed 3D classification of...
File | emd_12139_additional_2.map | ||||||||||||
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Annotation | Focussed mask used for focussed 3D classification of ACP domain density. The mask only covers the region of the map containing ACP density. This mask was not used for sharpening. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1.
File | emd_12139_half_map_1.map | ||||||||||||
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Annotation | Half map 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2.
File | emd_12139_half_map_2.map | ||||||||||||
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Annotation | Half map 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Fatty acid synthase
Entire | Name: Fatty acid synthase |
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Components |
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-Supramolecule #1: Fatty acid synthase
Supramolecule | Name: Fatty acid synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Komagataella phaffii GS115 (fungus) |
Molecular weight | Theoretical: 2.6 MDa |
-Macromolecule #1: Fatty acid synthase subunit alpha
Macromolecule | Name: Fatty acid synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: fatty-acyl-CoA synthase system |
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Source (natural) | Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 |
Molecular weight | Theoretical: 206.375734 KDa |
Sequence | String: MRPEVEQELS HVLLTELLAY QFASPVRWIE TQDVFLKDYN TERVVEIGPS PTLAGMASRT IKAKYESYDA ALSLQRQVLC YAKDTKEIY YTPDPADIAP PIKEEAETSA AATSSSAPAA AAPVSAAPAA APSGPVAEIP DEPVKAALVL HVLVAHKLKK S LDAVPLSK ...String: MRPEVEQELS HVLLTELLAY QFASPVRWIE TQDVFLKDYN TERVVEIGPS PTLAGMASRT IKAKYESYDA ALSLQRQVLC YAKDTKEIY YTPDPADIAP PIKEEAETSA AATSSSAPAA AAPVSAAPAA APSGPVAEIP DEPVKAALVL HVLVAHKLKK S LDAVPLSK AIKDLVGGKS TVQNEILGDL GKEFGSTPEK PEDTPLQELA EQFQDTFPGS LGKQTGSLVN RLMSSKMPGG FS LSVARKY LQTRWGLGPG RQDSVLLVAL VNEPGARLSS DGEAKEFLDS CAQKYASGAG ITLAQAAAGG AGSSGAGGAV IDA EAFEEL TKDNRVLARQ QLEVLARYLK YDLTKGEKSL VKEKEASSLL QQELDLWAEE HGEIYAQGIK PVFSHLKART YDSY WNWAR QDALSMYFDI IFGKLTDVDR ETVSQCIQLM NRSNPTLIKF MQYHIDHCPE YKGETYQLAK SLGQQLIDNC IQVAN QDPV YKDISYPTGP HTEVDSKGNI VYKEVNRKSV RKLEQYVFEM SQGGELTKEV QPTIQEDLAK IYEALNKQAS TESQLE FNK LYNSLIEFVE KSKEIEVSKS INAVLASKSS DSDRSAEISS LSEKTSIVDP VSGGIPPETV PFLHLKKKLP SGEWVFD RD TSALFLDGLQ KGAVNGISYK GKNVLITGAG AGSIGAEVLQ GLISGGAKVI VTTSRFSKKV TEYYQDIYAR FGAAGSCL I VVPFNQGSKQ DVEALIDYIY RDVKDEGLGW DLDAVIPFAA IPEAGIEIDE LGSKSELAHR IMLTNLLRLL GEVKKQKFT RAINTRPAQI ILPLSPNHGT FGSDGLYSES KLGLETLFNR WYSESWSEQL TVCGAIIGWT RGTGLMSGNN IIAEGLEKLG VRTFSQKEM AFNILGLMTP ELTEMCQNGP VVADLNGGLQ FIENLREYTA QLRNEIYETS EVRRAVSIET GIETRVVNGE N ADAPYQKA RIEPRANLKF EFPPLKSHKE IQNKAPGLEG LLDLERVIVV TGFGEVSPWG NTRTRWEMEA FGEFSIEGCL EM AWIMGFI KYHNGNLKGK PYTGWIDAKT NEPVEDKDIK KKYEEEILAH AGIRLIEPEL FRGYNPEKKE LIQEVIIEQD MAP FVTDES TAQQYKLQHE DAVDILKSEE SDEYTVTFKK GARLFVPKAL RFDRLVAGQI PTGWDAKRYG ISEDTISQVD PVTL YALVS TIEALLSAGI TDPYEFYKYV HVSEVGNCSG SGMGGVSALR GMFRDRYSDK PVQNDILQES FINTMSAWVN MLLLS SSGP IKTPVGACAT AVESVDIGVE TILSGKAKIC LVGGYDDFQE EGSYEFANMN ATSNSLDEFD HGRTPQEMSR PATTTR NGF MEAQGSGTQV IMNAELAIKM GVPIYAIVAL TATATDKIGR SVPAPGKGIL TTAREHHGSL KTKSPKLDIK YRTRQLN KR KDQIKQWVED ELEYIREEAA ELANSDAKFD AVSFVSERTE EVYREATKQV KMAQQEWGNE FWKNDPRIAP LRGALATF N LTVDDLGVAS FHGTSTKAND KNESITINKM MQHLGRSEGN PVFGVFQKYL TGHPKGAAGA WMLNGAIQIL QTGIVPGNR NADNVDKILE DFEYVLYPSR SIQTDGIKAC SVTSFGFGQK GGQAIVVHPD YLFASLDSET FEEYKTKVEA RYKSTYRYMH NAIIRNTMF VAKSDPPYTD ELEQPVYLDP LARVNNCKKN PSKLVFVNAD VQSKQNFVGK SANDTAKVIS SLTSDVTSGG K GVGVDVEL ISAINNENHT FIERNFTENE ISYCASAPSS KSSLAGTWSA KEAVFKALGV ESKGAGASLK DIEIVRDSKG AP TVVLHGD AKSAASAAGV KNVKVSISHD DVQSVAVAIS EF UniProtKB: Fatty acid synthase subunit alpha |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Details: PBS |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 281 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 60.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |