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- EMDB-46555: Atomic model of Ketoacyl Reductase domain and 4 helical bundle of... -

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Basic information

Entry
Database: EMDB / ID: EMD-46555
TitleAtomic model of Ketoacyl Reductase domain and 4 helical bundle of S. cerevisiae Fatty Acid Synthase (FAS) in complex with octanoyl-CoA (in vitro binding)
Map dataSharpened map
Sample
  • Complex: Fatty acid synthase
    • Protein or peptide: Fatty acid synthase subunit beta
    • Protein or peptide: Fatty acid synthase subunit alpha
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] octanethioate
  • Ligand: water
Keywordsoctanoyl-CoA / FAS / allosteric inhibition / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


fatty-acyl-CoA synthase system / fatty acid synthase complex / fatty-acyl-CoA synthase activity / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / holo-[acyl-carrier-protein] synthase activity / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity ...fatty-acyl-CoA synthase system / fatty acid synthase complex / fatty-acyl-CoA synthase activity / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / holo-[acyl-carrier-protein] synthase activity / enoyl-[acyl-carrier-protein] reductase (NADPH) 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 / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-[ACP] hydrolase activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / long-chain fatty acid biosynthetic process / fatty acid synthase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / lipid droplet / magnesium ion binding / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Fatty acid synthase beta subunit AflB /Fas1-like, fungi / 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 subunit beta, insertion 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 subunit alpha, acyl carrier domain ...Fatty acid synthase beta subunit AflB /Fas1-like, fungi / 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 subunit beta, insertion 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 subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / Fatty acid synthase type I, helical / : / Fatty acid synthase type I helical domain / : / Fatty acid synthase / N-terminal of MaoC-like dehydratase / FAS1-like, dehydratase domain region / 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 / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / HotDog domain superfamily / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site. / 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: 2.61 Å
AuthorsHasan NSM / Keszei FAA / Mazhab-Jafari MT
Funding support Canada, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)419240 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-06070 Canada
CitationJournal: To Be Published
Title: Allosteric Regulation of Ketoacyl Reduction in Fungal Fatty Acid Synthases
Authors: Hasan NSM / Keszei FAA / Mazhab-Jafari MT
History
DepositionAug 12, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46555.png

Downloads & links

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Map

FileDownload / File: emd_46555.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 324 pix.
= 333.72 Å		1.03 Å/pix.
x 324 pix.
= 333.72 Å		1.03 Å/pix.
x 324 pix.
= 333.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-5.5791335 - 8.159768
Average (Standard dev.)0.0052100024 (±0.37852576)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 333.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_46555_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_46555_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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 beta
    • Protein or peptide: Fatty acid synthase subunit alpha
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] octanethioate
  • Ligand: water

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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: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 2.6 MDa

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Macromolecule #1: Fatty acid synthase subunit beta

MacromoleculeName: Fatty acid synthase subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: fatty-acyl-CoA synthase system
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 228.83825 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 KGATGHAQGL 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 EVVFYAGMTM 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 #2: Fatty acid synthase subunit alpha

MacromoleculeName: Fatty acid synthase subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO / EC number: fatty-acyl-CoA synthase system
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 207.152359 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 AATSVESVDI 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 #3: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 6 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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Macromolecule #4: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...

MacromoleculeName: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] octanethioate
type: ligand / ID: 4 / Number of copies: 6 / Formula: SXO
Molecular weightTheoretical: 484.544 Da
Chemical component information

ChemComp-SXO:
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] octanethioate

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 3060 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
GridModel: Homemade / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 30 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 615912
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ta1

Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 535715
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelPDB ID:

6ta1


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9d4a:
Atomic model of Ketoacyl Reductase domain and 4 helical bundle of S. cerevisiae Fatty Acid Synthase (FAS) in complex with octanoyl-CoA (in vitro binding)

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