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- EMDB-17859: Asymmetric unit of the yeast fatty acid synthase in rotated state... -

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Basic information

Entry
Database: EMDB / ID: EMD-17859
TitleAsymmetric unit of the yeast fatty acid synthase in rotated state with ACP at the acetyl transferase domain (FASx sample)
Map data
Sample
  • Complex: Yeast fatty acid synthase
    • Protein or peptide: Fatty acid synthase subunit beta
  • Protein or peptide: Fatty acid synthase subunit alpha
  • Ligand: 4'-PHOSPHOPANTETHEINEPhosphopantetheine
  • Ligand: FLAVIN MONONUCLEOTIDE
KeywordsFatty acid synthase / acyl carrier protein / FAS / ACP / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


: / fatty-acyl-CoA synthase system / : / fatty-acyl-CoA synthase activity / fatty acid synthase complex / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase activity / oleoyl-[acyl-carrier-protein] hydrolase ...: / fatty-acyl-CoA synthase system / : / fatty-acyl-CoA synthase activity / fatty acid synthase complex / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase activity / oleoyl-[acyl-carrier-protein] hydrolase / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / holo-[acyl-carrier-protein] synthase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / fatty acid synthase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / 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) / long-chain fatty acid biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / lipid droplet / magnesium ion binding / mitochondrion / cytosol / cytoplasm
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 / Phosphopantetheine attachment site. / 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 speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSingh K / Bunzel G / Graf B / Yip KM / Stark H / Chari A
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Cell / Year: 2023
Title: Reconstruction of a fatty acid synthesis cycle from acyl carrier protein and cofactor structural snapshots.
Authors: Kashish Singh / Georg Bunzel / Benjamin Graf / Ka Man Yip / Meina Neumann-Schaal / Holger Stark / Ashwin Chari /
Abstract: Fatty acids (FAs) play a central metabolic role in living cells as constituents of membranes, cellular energy reserves, and second messenger precursors. A 2.6 MDa FA synthase (FAS), where the ...Fatty acids (FAs) play a central metabolic role in living cells as constituents of membranes, cellular energy reserves, and second messenger precursors. A 2.6 MDa FA synthase (FAS), where the enzymatic reactions and structures are known, is responsible for FA biosynthesis in yeast. Essential in the yeast FAS catalytic cycle is the acyl carrier protein (ACP) that actively shuttles substrates, biosynthetic intermediates, and products from one active site to another. We resolve the S. cerevisiae FAS structure at 1.9 Å, elucidating cofactors and water networks involved in their recognition. Structural snapshots of ACP domains bound to various enzymatic domains allow the reconstruction of a full yeast FA biosynthesis cycle. The structural information suggests that each FAS functional unit could accommodate exogenous proteins to incorporate various enzymatic activities, and we show proof-of-concept experiments where ectopic proteins are used to modulate FAS product profiles.
History
DepositionJul 13, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17859.png

Downloads & links

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Map

FileDownload / File: emd_17859.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.055 Å
Density
Contour LevelBy AUTHOR: 0.037
Minimum - Maximum-0.12494194 - 0.25018772
Average (Standard dev.)-0.0020453942 (±0.0131183015)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 253.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_17859_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_17859_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 : Yeast fatty acid synthase

EntireName: Yeast fatty acid synthase
Components
  • Complex: Yeast fatty acid synthase
    • Protein or peptide: Fatty acid synthase subunit beta
  • Protein or peptide: Fatty acid synthase subunit alpha
  • Ligand: 4'-PHOSPHOPANTETHEINEPhosphopantetheine
  • Ligand: FLAVIN MONONUCLEOTIDE

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Supramolecule #1: Yeast fatty acid synthase

SupramoleculeName: Yeast fatty acid synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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: 2 / Enantiomer: LEVO / EC number: fatty-acyl-CoA synthase system
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 207.184422 KDa
SequenceString: MKPEVEQELA HILLTELLAY QFASPVRWIE TQDVFLKDFN TERVVEIGPS PTLAGMAQRT LKNKYESYDA ALSLHREILC YSKDAKEIY YTPDPSELAA KEEPAKEEAP APTPAASAPA PAAAAPAPVA AAAPAAAAAE IADEPVKASL LLHVLVAHKL K KSLDSIPM ...String:
MKPEVEQELA HILLTELLAY QFASPVRWIE TQDVFLKDFN TERVVEIGPS PTLAGMAQRT LKNKYESYDA ALSLHREILC YSKDAKEIY YTPDPSELAA KEEPAKEEAP APTPAASAPA PAAAAPAPVA AAAPAAAAAE IADEPVKASL LLHVLVAHKL K KSLDSIPM SKTIKDLVGG KSTVQNEILG DLGKEFGTTP EKPEETPLEE LAETFQDTFS GALGKQSSSL LSRLISSKMP GG FTITVAR KYLQTRWGLP SGRQDGVLLV ALSNEPAARL GSEADAKAFL DSMAQKYASI VGVDLSSAAS ASGAAGAGAA AGA AMIDAG ALEEITKDHK VLARQQLQVL ARYLKMDLDN GERKFLKEKD TVAELQAQLD YLNAELGEFF VNGVATSFSR KKAR TFDSS WNWAKQSLLS LYFEIIHGVL KNVDREVVSE AINIMNRSND ALIKFMEYHI SNTDETKGEN YQLVKTLGEQ LIENC KQVL DVDPVYKDVA KPTGPKTAID KNGNITYSEE PREKVRKLSQ YVQEMALGGP ITKESQPTIE EDLTRVYKAI SAQADK QDI SSSTRVEFEK LYSDLMKFLE SSKEIDPSQT TQLAGMDVED ALDKDSTKEV ASLPNKSTIS KTVSSTIPRE TIPFLHL RK KTPAGDWKYD RQLSSLFLDG LEKAAFNGVT FKDKYVLITG AGKGSIGAEV LQGLLQGGAK VVVTTSRFSK QVTDYYQS I YAKYGAKGST LIVVPFNQGS KQDVEALIEF IYDTEKNGGL GWDLDAIIPF AAIPEQGIEL EHIDSKSEFA HRIMLTNIL RMMGCVKKQK SARGIETRPA QVILPMSPNH GTFGGDGMYS ESKLSLETLF NRWHSESWAN QLTVCGAIIG WTRGTGLMSA NNIIAEGIE KMGVRTFSQK EMAFNLLGLL TPEVVELCQK SPVMADLNGG LQFVPELKEF TAKLRKELVE TSEVRKAVSI E TALEHKVV NGNSADAAYA QVEIQPRANI QLDFPELKPY KQVKQIAPAE LEGLLDLERV IVVTGFAEVG PWGSARTRWE ME AFGEFSL EGCVEMAWIM GFISYHNGNL KGRPYTGWVD SKTKEPVDDK DVKAKYETSI LEHSGIRLIE PELFNGYNPE KKE MIQEVI VEEDLEPFEA SKETAEQFKH QHGDKVDIFE IPETGEYSVK LLKGATLYIP KALRFDRLVA GQIPTGWNAK TYGI SDDII SQVDPITLFV LVSVVEAFIA SGITDPYEMY KYVHVSEVGN CSGSGMGGVS ALRGMFKDRF KDEPVQNDIL QESFI NTMS AWVNMLLISS SGPIKTPVGA CATSVESVDI GVETILSGKA RICIVGGYDD FQEEGSFEFG NMKATSNTLE EFEHGR TPA EMSRPATTTR NGFMEAQGAG IQIIMQADLA LKMGVPIYGI VAMAATATDK IGRSVPAPGK GILTTAREHH SSVKYAS PN LNMKYRKRQL VTREAQIKDW VENELEALKL EAEEIPSEDQ NEFLLERTRE IHNEAESQLR AAQQQWGNDF YKRDPRIA P LRGALATYGL TIDDLGVASF HGTSTKANDK NESATINEMM KHLGRSEGNP VIGVFQKFLT GHPKGAAGAW MMNGALQIL NSGIIPGNRN ADNVDKILEQ FEYVLYPSKT LKTDGVRAVS ITSFGFGQKG GQAIVVHPDY LYGAITEDRY NEYVAKVSAR EKSAYKFFH NGMIYNKLFV SKEHAPYTDE LEEDVYLDPL ARVSKDKKSG SLTFNSKNIQ SKDSYINANT IETAKMIENM T KEKVSNGG VGVDVELITS INVENDTFIE RNFTPQEIEY CSAQPSVQSS FAGTWSAKEA VFKSLGVKSL GGGAALKDIE IV RVNKNAP AVELHGNAKK AAEEAGVTDV KVSISHDDLQ AVAVAVSTKK

UniProtKB: Fatty acid synthase subunit alpha

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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: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 228.940375 KDa
SequenceString: MDAYSTRPLT LSHGSLEHVL LVPTASFFIA SQLQEQFNKI LPEPTEGFAA DDEPTTPAEL VGKFLGYVSS LVEPSKVGQF DQVLNLCLT EFENCYLEGN DIHALAAKLL QENDTTLVKT KELIKNYITA RIMAKRPFDK KSNSALFRAV GEGNAQLVAI F GGQGNTDD ...String:
MDAYSTRPLT LSHGSLEHVL LVPTASFFIA SQLQEQFNKI LPEPTEGFAA DDEPTTPAEL VGKFLGYVSS LVEPSKVGQF DQVLNLCLT EFENCYLEGN DIHALAAKLL QENDTTLVKT KELIKNYITA RIMAKRPFDK KSNSALFRAV GEGNAQLVAI F GGQGNTDD YFEELRDLYQ TYHVLVGDLI KFSAETLSEL IRTTLDAEKV FTQGLNILEW LENPSNTPDK DYLLSIPISC PL IGVIQLA HYVVTAKLLG FTPGELRSYL KGATGHSQGL VTAVAIAETD SWESFFVSVR KAITVLFFIG VRCYEAYPNT SLP PSILED SLENNEGVPS PMLSISNLTQ EQVQDYVNKT NSHLPAGKQV EISLVNGAKN LVVSGPPQSL YGLNLTLRKA KAPS GLDQS RIPFSERKLK FSNRFLPVAS PFHSHLLVPA SDLINKDLVK NNVSFNAKDI QIPVYDTFDG SDLRVLSGSI SERIV DCII RLPVKWETTT QFKATHILDF GPGGASGLGV LTHRNKDGTG VRVIVAGTLD INPDDDYGFK QEIFDVTSNG LKKNPN WLE EYHPKLIKNK SGKIFVETKF SKLIGRPPLL VPGMTPCTVS PDFVAATTNA GYTIELAGGG YFSAAGMTAA IDSVVSQ IE KGSTFGINLI YVNPFMLQWG IPLIKELRSK GYPIQFLTIG AGVPSLEVAS EYIETLGLKY LGLKPGSIDA ISQVINIA K AHPNFPIALQ WTGGRGGGHH SFEDAHTPML QMYSKIRRHP NIMLIFGSGF GSADDTYPYL TGEWSTKFDY PPMPFDGFL FGSRVMIAKE VKTSPDAKKC IAACTGVPDD KWEQTYKKPT GGIVTVRSEM GEPIHKIATR GVMLWKEFDE TIFNLPKNKL VPTLEAKRD YIISRLNADF QKPWFATVNG QARDLATMTY EEVAKRLVEL MFIRSTNSWF DVTWRTFTGD FLRRVEERFT K SKTLSLIQ SYSLLDKPDE AIEKVFNAYP AAREQFLNAQ DIDHFLSMCQ NPMQKPVPFV PVLDRRFEIF FKKDSLWQSE HL EAVVDQD VQRTCILHGP VAAQFTKVID EPIKSIMDGI HDGHIKKLLH QYYGDDESKI PAVEYFGGES PVDVQSQVDS SSV SEDSAV FKATSSTDEE SWFKALAGSE INWRHASFLC SFITQDKMFV SNPIRKVFKP SQGMVVEISN GNTSSKTVVT LSEP VQGEL KPTVILKLLK ENIIQMEMIE NRTMDGKPVS LPLLYNFNPD NGFAPISEVM EDRNQRIKEM YWKLWIDEPF NLDFD PRDV IKGKDFEITA KEVYDFTHAV GNNCEDFVSR PDRTMLAPMD FAIVVGWRAI IKAIFPNTVD GDLLKLVHLS NGYKMI PGA KPLQVGDVVS TTAVIESVVN QPTGKIVDVV GTLSRNGKPV MEVTSSFFYR GNYTDFENTF QKTVEPVYQM HIKTSKD IA VLRSKEWFQL DDEDFDLLNK TLTFETETEV TFKNANIFSS VKCFGPIKVE LPTKETVEIG IVDYEAGASH GNPVVDFL K RNGSTLEQKV NLENPIPIAV LDSYTPSTNE PYARVSGDLN PIHVSRHFAS YANLPGTITH GMFSSASVRA LIENWAADS VSSRVRGYTC QFVDMVLPNT ALKTSIQHVG MINGRKLIKF ETRNEDDVVV LTGEAEIEQP VTTFVFTGQG SQEQGMGMDL YKTSKAAQD VWNRADNHFK DTYGFSILDI VINNPVNLTI HFGGEKGKRI RENYSAMIFE TIVDGKLKTE KIFKEINEHS T SYTFRSEK GLLSATQFTQ PALTLMEKAA FEDLKSKGLI PADATFAGHS LGEYAALASL ADVMSIESLV EVVFYRGMTM QV AVPRDEL GRSNYGMIAI NPGRVAASFS QEALQYVVER VGKRTGWLVE IVNYNVENQQ YVAAGDLRAL DTVTNVLNFI KLQ KIDIIE LQKSLSLEEV EGHLFEIIDE ASKKSAVKPR PLKLERGFAC IPLVGISVPF HSTYLMNGVK PFKSFLKKNI IKEN VKVAR LAGKYIPNLT AKPFQVTKEY FQDVYDLTGS EPIKEIIDNW EKYEQS

UniProtKB: Fatty acid synthase subunit beta

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Macromolecule #3: 4'-PHOSPHOPANTETHEINE

MacromoleculeName: 4'-PHOSPHOPANTETHEINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: PNS
Molecular weightTheoretical: 358.348 Da
Chemical component information

ChemComp-PNS:
4'-PHOSPHOPANTETHEINE / Phosphopantetheine

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Macromolecule #4: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 4 / 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: 6.5
VitrificationCryogen name: ETHANE

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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: 25.0 µm / Nominal defocus min: 5.0 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

4578

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 196527

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