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- EMDB-46553: Atomic model of Ketoacyl Reductase domain and 4 helical bundle of... -

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Basic information

Entry
Database: EMDB / ID: EMD-46553
TitleAtomic model of Ketoacyl Reductase domain and 4 helical bundle of Candida albicans Fatty Acid Synthase (FAS) in complex with Palmitoyl-CoA (in vivo 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: water
KeywordsPalmitoyl-CoA / FAS / allosteric inhibition / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


mitotic nuclear membrane biogenesis / palmitic acid biosynthetic process / 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 ...mitotic nuclear membrane biogenesis / palmitic acid biosynthetic process / 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 / cytosol
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 speciesCandida albicans (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 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_46553.png

Downloads & links

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Map

FileDownload / File: emd_46553.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: 0.7
Minimum - Maximum-4.458977 - 6.7540555
Average (Standard dev.)0.009332942 (±0.27263415)
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_46553_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_46553_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: 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: Candida albicans (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: Candida albicans (yeast)
Molecular weightTheoretical: 228.177609 KDa
SequenceString: MSTHRPFQLT HGSIEHTLLV PNDLFFNYSQ LKDEFIKTLP EPTEGFAGDD EPSSPAELYG KFIGFISNAQ FPQIVELSLK DFESRFLDN NNDNIHSFAV KLLDDETYPT TIAKVKENIV KNYYKAVKSI NKVESNLLYH CKHDAKLVAI FGGQGNTDDY F EELRELYT ...String:
MSTHRPFQLT HGSIEHTLLV PNDLFFNYSQ LKDEFIKTLP EPTEGFAGDD EPSSPAELYG KFIGFISNAQ FPQIVELSLK DFESRFLDN NNDNIHSFAV KLLDDETYPT TIAKVKENIV KNYYKAVKSI NKVESNLLYH CKHDAKLVAI FGGQGNTDDY F EELRELYT LYQGLIEDLL VSIAEKLNQL HPSFDKIYTQ GLNILSWLKH PETTPDQDYL LSVPVSCPVI CVIQLCHYTI TC KVLGLTP GEFRNSLKWS TGHSQGLVTA VTIAASDSWD SFLKNSLTAV SLLLFIGSRC LSTYPRTSLP PTMLQDSLDN GEG RPSPML SVRDLSIKQV EKFIEQTNSH LPREKHIAIS LINGARNLVL SGPPESLYGF NLNLRNQKAP MGLDQSRVPF SERK LKCSN RFLPIFAPFH SHLLADATEL ILDDVKEHGL SFEGLKIPVY DTFDGSDFQA LKEPIIDRVV KLITELPVHW EEATN HKAT HILDFGPGGV SGLGVLTHRN KEGTGARIIL AGTLDSNPID DEYGFKHEIF QTSADKAIKW APDWLKELRP TLVKNS EGK IYVKTKFSQL LGRAPLMVAG MTPTTVNTDI VSASLNAGYH IELAGGGYFS PVMMTRAIDD IVSRIKPGYG LGINLIY VN PFMLQWGIPL IKDLREKGYP IQSLTIGAGV PSIEVATEYI EDLGLTHLGL KPGSVDAISQ VIAIAKAHPT FPIVLQWT G GRGGGHHSFE DFHQPIIQMY SKIRRCSNIV LVAGSGFGSD EDTYPYLSGY WSEKFNYPPM PFDGVLFGSR VMTSKESHT SLAAKKLIVE CKGVPDQQWE QTYKKPTGGI ITVRSEMGEP IHKIATRGVM FWKELDDTIF NLPKNKLLDA LNKKRDHIIK KLNNDFQKP WFGKNANGVC DLQEMTYKEV ANRLVELMYV KKSHRWIDVS LRNMYGDFLR RVEERFTSSA GTVSLLQNFN Q LNEPEQFT ADFFEKFPQA GKQLISEEDC DYFLMLAARP GQKPVPFVPV LDERFEFFFK KDSLWQSEDL ESVVDEDVQR TC ILHGPVA SQYTSKVDEP IGDILNSIHE GHIARLIKEE YAGDESKIPV VEYFGGKKPA SVSATSVNII DGNQVVYEID SEL PNKQEW LDLLAGTELN WLQAFISTDR IVQGSKHVSN PLHDILTPAK HSKVTIDKKT KKLTAFENIK GDLLPVVEIE LVKP NTIQL SLIEHRTADT NPVALPFLYK YNPADGFAPI LEIMEDRNER IKEFYWKLWF GSSVPYSNDI NVEKAILGDE ITISS QTIS EFTHAIGNKC DAFVDRPGKA TLAPMDFAIV IGWKAIIKAI FPKSVDGDLL KLVHLSNGYK MITGAAPLKK GDVVST KAE IKAVLNQPSG KLVEVVGTIY REGKPVMEVT SQFLYRGEYN DYCNTFQKVT ETPVQVAFKS AKDLAVLRSK EWFHLEK DV QFDVLTFRCE STYKFKSANV YSSIKTTGQV LLELPTKEVI QVGSVDYEAG TSYGNPVTDY LSRNGKTIEE SVIFENAI P LSSGEELTSK APGTNEPYAI VSGDYNPIHV SRVFAAYAKL PGTITHGMYS SASIRALVEE WAANNVAARV RAFKCDFVG MVLPNDTLQT TMEHVGMING RKIIKVETRN VETELPVLIG EAEIEQPTTT YVFTGQGSQE QGMGMELYNS SEVAREVWDK ADRHFVNNY GFSILDIVQN NPNELTIHFG GAKGRAIRDN YIGMMFETIG EDGALKSEKI FKDIDETTTS YTFVSPTGLL S ATQFTQPA LTLMEKAAYE DIKSKGLIPS DIMFAGHSLG EYSALSSLAN VMPIESLVDV VFYRGMTMQV AVPRDELGRS NY GMVAVNP SRVSATFDDS ALRFVVDEVA NKTKWLLEIV NYNVENQQYV AAGDLRALDT LTNVLNVLKI NKIDIVKLQE QMS IEKVKE HLYEIVDEVA AKSLAKPQPI DLERGFAVIP LKGISVPFHS SYLMSGVKPF QRFLCKKIPK SSVKPQDLIG KYIP NLTAK PFELTKEYFQ SVYDLTKSEK IKSILDNWEQ YE

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: Candida albicans (yeast)
Molecular weightTheoretical: 207.825703 KDa
SequenceString: MKPEIEQELS HTLLTELLAY QFASPVRWIE TQDVFLKQHN TERIIEIGPS PTLAGMANRT IKAKYESYDA ALSLQRQVLC YSKDAKEIY YKPDPADLAP KETPKQEEST PSAPAAATPT PAAAAAPTPA PAPASAGPVE SIPDEPVKAN LLIHVLVAQK L KKPLDAVP ...String:
MKPEIEQELS HTLLTELLAY QFASPVRWIE TQDVFLKQHN TERIIEIGPS PTLAGMANRT IKAKYESYDA ALSLQRQVLC YSKDAKEIY YKPDPADLAP KETPKQEEST PSAPAAATPT PAAAAAPTPA PAPASAGPVE SIPDEPVKAN LLIHVLVAQK L KKPLDAVP MTKAIKDLVN GKSTVQNEIL GDLGKEFGST PEKPEDTPLE ELAEQFQDSF SGQLGKTSTS LIGRLMSSKM PG GFSITTA RKYLESRFGL GAGRQDSVLL MALTNEPANR LGSEADAKTF FDGIAQKYAS SAGISLSSGA GSGAGAANSG GAV VDSAAL DALTAENKKL AKQQLEVLAR YLQSRLKQGS LKSFIKEKEA SAVLQKELDL WEAEHGEFYA KGIQPTFSAL KSRT YDSYW NWARQDVLSM YFDIIFGKLT SVDRETINQC IQIMNRANPT LIKFMQYHID HCPEYKGETY KLAKRLGQQL IDNCK QVLT EDPVYKDVSR ITGPKTKVSA KGNIEYEETQ KDSVRKFEQY VYEMAQGGAM TKVSQPTIQE DLARVYKAIS KQASKD SKL ELQRVYEDLL KVVESSKEIE TEQLTKDILQ AATVPTTPTE EVDDPCTPSS DDEIASLPDK TSIIQPVSST IPSQTIP FL HIQKKTKDGW EYNKKLSSLY LDGLESAAIN GLTFKDKYVL VTGAGAGSIG AEILQGLISG GAKVIVTTSR FSKKVTEY Y QNMYARYGAA GSTLIVVPFN QGSKQDVDAL VQYIYDEPKK GGLGWDLDAI IPFAAIPENG NGLDNIDSKS EFAHRIMLT NLLRLLGAVK SKKPTDTRPA QCILPLSPNH GTFGFDGLYS ESKISLETLF NRWYSEDWGS KLTVCGAVIG WTRGTGLMSA NNIIAEGIE KLGVRTFSQK EMAFNILGLL TPEIVQLCQE EPVMADLNGG LQFIDNLKDF TSKLRTDLLE TADIRRAVSI E SAIEQKVV NGDNVDANYS KVMVEPRANM KFDFPTLKSY DEIKQIAPEL EGMLDLENVV VVTGFAEVGP WGNSRTRWEM EA YGEFSLE GAIEMAWIMG FIKYHNGNLQ GKPYSGWVDA KTQTPIDEKD IKSKYEEEIL EHSGIRLIEP ELFNGYDPKK KQM IQEIVV QHDLEPFECS KETAEQYKHE HGEKCEIFEI EESGEYTVRI LKGATLYVPK ALRFDRLVAG QIPTGWDART YGIP EDTIS QVDPITLYVL VATVEALLSA GITDPYEFYK YVHVSEVGNC SGSGMGGVSA LRGMFKDRYA DKPVQNDILQ ESFIN TMSA WVNMLLLSSS GPIKTPVGAC ATAVESVDIG IETILSGKAK VVLVGGYDDF QEEGSYEFAN MNATSNSIEE FKHGRT PKE MSRPTTTTRN GFMEAQGSGI QVIMTADLAL KMGVPIHAVL AMTATATDKI GRSVPAPGKG ILTTAREHHG NLKYPSP LL NIKYRKRQLN KRLEQIKSWE ETELSYLQEE AELAKEEFGD EFSMHEFLKE RTEEVYRESK RQVSDAKKQW GNSFYKSD P RIAPLRGALA AFNLTIDDIG VASFHGTSTV ANDKNESATI NNMMKHLGRS EGNPVFGVFQ KYLTGHPKGA AGAWMLNGA IQILESGLVP GNRNADNVDK LLEQYEYVLY PSRSIQTDGI KAVSVTSFGF GQKGAQAVVV HPDYLFAVLD RSTYEEYATK VSARNKKTY RYMHNAITRN TMFVAKDKAP YSDELEQPVY LDPLARVEEN KKKLVFSDKT IQSNQSYVGE VAQKTAKALS T LNKSSKGV GVDVELLSAI NIDNETFIER NFTGNEVEYC LNTAHPQASF TGTWSAKEAV FKALGVESKG AGASLIDIEI TR DVNGAPK VILHGEAKKA AAKAGVKNVN ISISHDDFQA TAVALSEF

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: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 2018 / 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: 277 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 51.2 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: 439246
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6u5v

Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 252339
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:

6u5v


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

PDB-9d48:
Atomic model of Ketoacyl Reductase domain and 4 helical bundle of Candida albicans Fatty Acid Synthase (FAS) in complex with Palmitoyl-CoA (in vivo binding)

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