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- EMDB-12138: Cryo-EM structure of fatty acid synthase (FAS) from Pichia pastoris -

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Basic information

Entry
Database: EMDB / ID: EMD-12138
TitleCryo-EM structure of fatty acid synthase (FAS) from Pichia pastoris
Map dataMap filtered according to local resolution.
Sample
  • Complex: Fatty acid synthase
    • Protein or peptide: Fatty acid synthase subunit alpha
    • Protein or peptide: Fatty acid synthase subunit beta
  • Ligand: FLAVIN MONONUCLEOTIDE
Function / homology
Function and homology information


mitotic nuclear membrane biogenesis / palmitic acid biosynthetic process / : / : / (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / fatty-acyl-CoA synthase system / : / fatty-acyl-CoA synthase activity / fatty acid synthase complex ...mitotic nuclear membrane biogenesis / palmitic acid biosynthetic process / : / : / (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / 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 / oleoyl-[acyl-carrier-protein] hydrolase / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / holo-[acyl-carrier-protein] synthase activity / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase 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 / fatty acid synthase activity / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / magnesium ion binding
Similarity search - Function
Fatty acid synthase, meander beta sheet domain / Fatty acid synthase subunit beta, N-terminal domain / : / N-terminal domain in fatty acid synthase subunit beta / Fatty acid synthase meander beta sheet domain / Fatty acid synthase beta subunit AflB /Fas1-like, fungi / Fatty acid synthase subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase alpha subunit, yeast ...Fatty acid synthase, meander beta sheet domain / Fatty acid synthase subunit beta, N-terminal domain / : / N-terminal domain in fatty acid synthase subunit beta / Fatty acid synthase meander beta sheet domain / Fatty acid synthase beta subunit AflB /Fas1-like, fungi / Fatty acid synthase subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase alpha subunit, yeast / Fatty acid synthase subunit beta/Fas1-like, helical / Fatty acid synthase type I, helical / Fatty acid synthase type I helical domain / Fatty acid synthase / N-terminal of MaoC-like dehydratase / N-terminal half of MaoC dehydratase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / MaoC-like dehydratase domain / MaoC like domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / HotDog domain superfamily / 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. / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Fatty acid synthase subunit beta / Fatty acid synthase subunit alpha
Similarity search - Component
Biological speciesKomagataella phaffii GS115 (fungus) / Yeast (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSnowden JS / Alzahrani J / Sherry L / Stacey M / Rowlands DJ / Ranson NA / Stonehouse NJ
Funding support United Kingdom, Saudi Arabia, 3 items
OrganizationGrant numberCountry
Wellcome Trust102174/B/13/Z United Kingdom
World Health Organization (WHO)2019/883397-O United Kingdom
Saudi Ministry of Education Saudi Arabia
CitationJournal: 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
DepositionDec 18, 2020-
Header (metadata) releaseMay 19, 2021-
Map releaseMay 19, 2021-
UpdateMay 19, 2021-
Current statusMay 19, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.072
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.072
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  • Surface view with fitted model
  • Atomic models: PDB-7bc4
  • Surface level: 0.072
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7bc4
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12138.png

Downloads & links

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Map

FileDownload / File: emd_12138.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap filtered according to local resolution.
Voxel sizeX=Y=Z: 1.065 Å
Density
Contour LevelBy AUTHOR: 0.072 / Movie #1: 0.072
Minimum - Maximum-0.30636075 - 0.53115934
Average (Standard dev.)8.148815e-05 (±0.014277468)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 489.90002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z460460460
origin x/y/z0.0000.0000.000
length x/y/z489.900489.900489.900
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS460460460
D min/max/mean-0.3060.5310.000

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Supplemental data

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Mask #1

Fileemd_12138_msk_1.map
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Additional map: Unsharpened map.

Fileemd_12138_additional_1.map
AnnotationUnsharpened map.
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Additional map: Map of local resolution values, for local resolution...

Fileemd_12138_additional_2.map
AnnotationMap of local resolution values, for local resolution colouring of maps.
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Additional map: Sharpened map without solvent mask applied.

Fileemd_12138_additional_3.map
AnnotationSharpened map without solvent mask applied.
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Additional map: Sharpened map with solvent mask applied.

Fileemd_12138_additional_4.map
AnnotationSharpened map with solvent mask applied.
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Half map: Half map 1.

Fileemd_12138_half_map_1.map
AnnotationHalf map 1.
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Half map: Half map 2.

Fileemd_12138_half_map_2.map
AnnotationHalf map 2.
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Sample components

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Entire : Fatty acid synthase

EntireName: Fatty acid synthase
Components
  • Complex: Fatty acid synthase
    • Protein or peptide: Fatty acid synthase subunit alpha
    • Protein or peptide: Fatty acid synthase subunit beta
  • Ligand: FLAVIN MONONUCLEOTIDE

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Supramolecule #1: Fatty acid synthase

SupramoleculeName: Fatty acid synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Komagataella phaffii GS115 (fungus)
Molecular weightTheoretical: 2.6 MDa

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Macromolecule #1: Fatty acid synthase subunit alpha

MacromoleculeName: Fatty acid synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: fatty-acyl-CoA synthase system
Source (natural)Organism: Yeast (yeast) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 206.375734 KDa
SequenceString: 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

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Macromolecule #2: Fatty acid synthase subunit beta

MacromoleculeName: Fatty acid synthase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: fatty-acyl-CoA synthase system
Source (natural)Organism: Yeast (yeast) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 230.000625 KDa
SequenceString: 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

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Macromolecule #3: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

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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: 7.4 / Details: PBS
GridMaterial: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 281 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 3643 / Average electron dose: 60.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
In silico model: Initial model generated using SGD in RELION 3.0.7.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.7)
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7) / Number images used: 37054
FSC plot (resolution estimation)

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