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- EMDB-12138: Cryo-EM structure of fatty acid synthase (FAS) from Pichia pastoris -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12138 | ||||||||||||
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Title | Cryo-EM structure of fatty acid synthase (FAS) from Pichia pastoris | ||||||||||||
![]() | Map filtered according to local resolution. | ||||||||||||
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Function / homology | ![]() mitotic nuclear membrane biogenesis / : / : / : / palmitic acid biosynthetic process / : / : / : / fatty-acyl-CoA synthase system / fatty-acyl-CoA synthase activity ...mitotic nuclear membrane biogenesis / : / : / : / palmitic acid biosynthetic process / : / : / : / fatty-acyl-CoA synthase system / fatty-acyl-CoA synthase activity / fatty acid synthase complex / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / oleoyl-[acyl-carrier-protein] hydrolase / : / holo-[acyl-carrier-protein] synthase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / fatty acid synthase activity / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / magnesium ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
![]() | Snowden JS / Alzahrani J / Sherry L / Stacey M / Rowlands DJ / Ranson NA / Stonehouse NJ | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 211.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29 KB 29 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.3 KB | Display | ![]() |
Images | ![]() | 216.3 KB | ||
Masks | ![]() | 371.3 MB | ![]() | |
Others | ![]() ![]() ![]() ![]() ![]() ![]() | 295.8 MB 186 MB 348.6 MB 48 MB 296.9 MB 298.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bc4MC ![]() 7bc5C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Map filtered according to local resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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-Additional map: Unsharpened map.
File | emd_12138_additional_1.map | ||||||||||||
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Annotation | Unsharpened map. | ||||||||||||
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-Additional map: Map of local resolution values, for local resolution...
File | emd_12138_additional_2.map | ||||||||||||
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Annotation | Map of local resolution values, for local resolution colouring of maps. | ||||||||||||
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-Additional map: Sharpened map without solvent mask applied.
File | emd_12138_additional_3.map | ||||||||||||
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Annotation | Sharpened map without solvent mask applied. | ||||||||||||
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-Additional map: Sharpened map with solvent mask applied.
File | emd_12138_additional_4.map | ||||||||||||
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Annotation | Sharpened map with solvent mask applied. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1.
File | emd_12138_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_12138_half_map_2.map | ||||||||||||
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Annotation | Half map 2. | ||||||||||||
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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: #1-#2 |
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Source (natural) | Organism: ![]() |
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: ![]() |
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 |
-Macromolecule #2: Fatty acid synthase subunit beta
Macromolecule | Name: Fatty acid synthase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: fatty-acyl-CoA synthase system |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 230.000625 KDa |
Sequence | String: MSATSGVVNR PLVLNHGSIE STILIPTTEY HFYQTLLEGF RKSLPQVTEG FADDDEPSSK AELLMKFLGY IVQSGVSNQQ EQLAAAKLV LNEFESRFLQ GLNLHSYAAI LLKSETFPTT LLKIKENLIK NYYLGRALVY LPGQRGLVYP PSALLNAGKS G SAQIYAIF ...String: MSATSGVVNR PLVLNHGSIE STILIPTTEY HFYQTLLEGF RKSLPQVTEG FADDDEPSSK AELLMKFLGY IVQSGVSNQQ EQLAAAKLV LNEFESRFLQ GLNLHSYAAI LLKSETFPTT LLKIKENLIK NYYLGRALVY LPGQRGLVYP PSALLNAGKS G SAQIYAIF GGQGNTDDYF EELRDIYHIY QGLVSDFVTK AQLKLQELIR TTPETDRIYT QGLDLINWLE NKDKTPDQQQ LL SIPMSCP LICVIQLCHY IVTCRILGIT PGQLRDSLKG TTGHSQGLVT AVVVSSADSW ESFEKLALQA VEFMFYIGVR GLQ TYPNTS LPPSIVQDSE ENAEGTPSPM LSVRDLSYDQ LVKFVNETNQ HLPEAKHIDI SLINGPRNVV LTGPPQSLYG LNLN LRKAK APSGLDQARI PFSERKLRFS NRFLPIMSPF HSHLLSPSTE KIVADLKKAG VEFSQSSMKL PVFDTYDGKD LRSYS GSIA ARLVECITKL RVNWELSTEF NSTHVLDFGP GGASGLGVLT HRNKEGTGSR VIVAGVLDAE SEDSEFGYKQ EIFESN EKA IKYAPNWLKE YKPKLVKTSA GKIFVDTKFS RLLGRAPLMV PGMTPTTVSP DFVAATLNAG FHTEIAGGGY FAPSIMK AA LQRVIDQVTP GTGVGINLIY VNPRMLQWGI PMIKELREQG FPIQSLSIGA GVPSLEVATE YIETLGLAHL GLKPGSID A VNQVITIAKA HPNFPIVLQW TGGRGGGHHS FEDFHQPILQ MYSKIRKCKN IILIAGSGFG SAEDTYPYLT GSWSHQFSY PSMPFDGVLF GSRVMTAKEA KTSPAAKQAI ADCTGVDNSQ WENTYKKPTG GIITVRSEMG EPIHKIATRG VMLWKELDDT IFTLPKNKM LEAIAKKKDY IIKKLNADYQ KPWFAKNEKG TCDLEDMTYK QIAERLVELM YVRKSQRWID VTLRNFTGKF L RRIEERFA TKVGTISLIQ NFSQLEEPEK AIDSVFKAYP EAASQLINEE DCDWFLLEAQ SPTQKPVPFI PVLDERFEFF FK KDSLWQS EDLEAVVGED VQRTCILHGP VAAQFSNKVD EPIKDILENI HKGHIKSLVK EVYNGDESKI PVVEYFSSVD SFS DTAIEG VKIERSRNTE TFTVTSGNVD NQQWFDLLAG KELSWRRAFI TAARLVQGTN FVSNPAHSVL APSKDLVVKI ENGS DAKKT VLTAFQRVRG KYVPAVSLKS IGDLKIKLEL IETRTADKSA VALELFYNYK PTDGFAPILE VMEGRNTSIK NFYWK LWFG SSVPVDLDFD ANKPISGGEA SVSSQAIAEF THAVGNSCED FVPRAGRPQL APMDFAIVLG WKAIMKAIFP KTVDGD ILK LVHLSNGYKM FPGADPLKKG DVVSTVAHIR SVVNGETGKT VEVVGVISRD GKPVLEVNSQ FFYRGKYQDF GNSFKKT TE TPVQVAFKSA KDIAVLKSKE WFHLEKDIDL LNQTLTFRCE SYVKFKSSTV FASVKTTGQA LLELPSKEII QVAEINYE S GSSYGNPVLD YLTRHGSTIE QPIMFENAIP LAQGTELTSK APGTNETYAA VSGDYNPIHV NKVFASYANL PGTITHGMY SSAAVRALVE QWAAQNVATR VRAFKADFVG MVLPNDELVT HLEHVGMING RKIIKVETKK VETEEVVLIG EAEIEQPVST FVFTGQGSQ EQGMGMDLYN SSEVAKSVWD RADVHFINNY GFSILDIVKN NPTELTVHFG GAKGRSIRNN YISMMFETVA A DGQLKSEK IFKEINEDTI SFTFKSPTGL LSATQFTQPA LTLMEKASFE DMKSKGLVPS ESMFAGHSLG EYSALTSLGD VM PIESLVD VVFYRGMTMQ VAVPRDEQGR SNYGMIAVNP SRVSSTFNDS ALRFVVEHIA QQTGWLLEIV NYNVENTQYV AAG DLRGLD TLSNVLNVFK IQKIDIVKLQ ETISLDEVKV HLSEIVDEVS KKSSSKPQPI DLERGFACIP LKGISVPFHS SYLR SGVKP FQTFLCKKIP KSAVKPANLI GKYIPNLTAK PFQLTKEYFE DVYELTKSEK IKHILDHWEE YESS |
-Macromolecule #3: FLAVIN MONONUCLEOTIDE
Macromolecule | Name: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 1 / Formula: FMN |
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Molecular weight | Theoretical: 456.344 Da |
Chemical component information | ![]() ChemComp-FMN: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 / Details: PBS |
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Grid | Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 281 K / Instrument: LEICA EM GP |
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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 / Number real images: 3643 / Average electron dose: 60.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
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 |