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- EMDB-20658: Electron cryomicroscopy structure of C. albicans FAS in the KS-st... -

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Basic information

Entry
Database: EMDB / ID: EMD-20658
TitleElectron cryomicroscopy structure of C. albicans FAS in the KS-stalled state
Map data
Sample
  • Complex: Fatty acid synthase
    • Protein or peptide: Fatty acid synthase subunit alpha
    • Protein or peptide: Fatty acid synthase subunit beta
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: FLAVIN MONONUCLEOTIDE
KeywordsFungal Fatty acid synthase / TRANSFERASE
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 / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase activity / : / oleoyl-[acyl-carrier-protein] hydrolase ...mitotic nuclear membrane biogenesis / palmitic acid biosynthetic process / fatty-acyl-CoA synthase system / fatty acid synthase complex / fatty-acyl-CoA synthase activity / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase activity / : / oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-[ACP] hydrolase activity / 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) / long-chain fatty acid biosynthetic process / fatty acid synthase activity / enoyl-[acyl-carrier-protein] reductase (NADH) 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 / 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 / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / 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: 3.3 Å
AuthorsLou JW / Mazhab-Jafari MT
CitationJournal: Sci Rep / Year: 2019
Title: Electron cryomicroscopy observation of acyl carrier protein translocation in type I fungal fatty acid synthase.
Authors: Jennifer W Lou / Kali R Iyer / S M Naimul Hasan / Leah E Cowen / Mohammad T Mazhab-Jafari /
Abstract: During fatty acid biosynthesis, acyl carrier proteins (ACPs) from type I fungal fatty acid synthase (FAS) shuttle substrates and intermediates within a reaction chamber that hosts multiple spatially- ...During fatty acid biosynthesis, acyl carrier proteins (ACPs) from type I fungal fatty acid synthase (FAS) shuttle substrates and intermediates within a reaction chamber that hosts multiple spatially-fixed catalytic centers. A major challenge in understanding the mechanism of ACP-mediated substrate shuttling is experimental observation of its transient interaction landscape within the reaction chamber. Here, we have shown that ACP spatial distribution is sensitive to the presence of substrates in a catalytically inhibited state, which enables high-resolution investigation of the ACP-dependent conformational transitions within the enoyl reductase (ER) reaction site. In two fungal FASs with distinct ACP localization, the shuttling domain is targeted to the ketoacyl-synthase (KS) domain and away from other catalytic centers, such as acetyl-transferase (AT) and ER domains by steric blockage of the KS active site followed by addition of substrates. These studies strongly suggest that acylation of phosphopantetheine arm of ACP may be an integral part of the substrate shuttling mechanism in type I fungal FAS.
History
DepositionAug 28, 2019-
Header (metadata) releaseOct 16, 2019-
Map releaseOct 16, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.704
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.704
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6u5w
  • Surface level: 0.704
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6u5w
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20658.png

Downloads & links

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Map

FileDownload / File: emd_20658.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 352 pix.
= 373.12 Å		1.06 Å/pix.
x 352 pix.
= 373.12 Å		1.06 Å/pix.
x 352 pix.
= 373.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.704 / Movie #1: 0.704
Minimum - Maximum-0.81721324 - 1.9417192
Average (Standard dev.)0.012240873 (±0.13309371)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 373.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z373.120373.120373.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.8171.9420.012

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Supplemental data

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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: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • 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: Candida albicans (yeast)
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: Candida albicans (yeast)
Molecular weightTheoretical: 190.261984 KDa
SequenceString: MKPEIEQELS HTLLTELLAY QFASPVRWIE TQDVFLKQHN TERIIEIGPS PTLAGMANRT IKAKYESYDA ALSLQRQVLC YSKDAKEIY YKPDPADLAP KETPKQEEST PSAPAAATPT PAAAAAPTPA PAPASAGPVE SSSGAGSGAG AANSGGAVVD S AALDALTA ...String:
MKPEIEQELS HTLLTELLAY QFASPVRWIE TQDVFLKQHN TERIIEIGPS PTLAGMANRT IKAKYESYDA ALSLQRQVLC YSKDAKEIY YKPDPADLAP KETPKQEEST PSAPAAATPT PAAAAAPTPA PAPASAGPVE SSSGAGSGAG AANSGGAVVD S AALDALTA ENKKLAKQQL EVLARYLQVD LNKGSAKSFI KEKEASAVLQ KELDLWEAEH GEFYAKGIQP TFSALKSRTY DS YWNWARQ DVLSMYFDII FGKLTSVDRE TINQCIQIMN RANPTLIKFM QYHIDHCPEY KGETYKLAKR LGQQLIDNCK QVL TEDPVY KDVSRITGPK TKVSAKGNIE YEETQKDSVR KFEQYVYEMA QGGAMTKVSQ PTIQEDLARV YKAISKQASK DSKL ELQRV YEDLLKVVES SKEIETEQLT KDILQAATVP TTPTEEVDDP CTPSSDDEIA SLPDKTSIIQ PVSSTIPSQT IPFLH IQKK TKDGWEYNKK LSSLYLDGLE SAAINGLTFK DKYVLVTGAG AGSIGAEILQ GLISGGAKVI VTTSRFSKKV TEYYQN MYA RYGAAGSTLI VVPFNQGSKQ DVDALVQYIY DEPKKGGLGW DLDAIIPFAA IPENGNGLDN IDSKSEFAHR IMLTNLL RL LGAVKSKKTT DTRPAQCILP LSPNHGTFGF DGLYSESKIS LETLFNRWYS EDWGSKLTVC GAVIGWTRGT GLMSANNI I AEGIEKLGVR TFSQKEMAFN ILGLLTPEIV QLCQEEPVMA DLNGGLQFID NLKDFTSKLR TDLLETADIR RAVSIESAI EQKVVNGDNV DANYSKVMVE PRANMKFDFP TLKSYDEIKQ IAPELEGMLD LENVVVVTGF AEVGPWGNSR TRWEMEAYGE FSLEGAIEM AWIMGFIKYH NGNLKGKPYS GWVDAKTQTP IDEKDIKSKY EEEILEHSGI RLIEPELFNG YDPKKKQMIQ E VVVQHDLE PFECSKETAE QYKHEHGEKC EIFEIEESGE YTVRILKGAT LYVPKALRFD RLVAGQIPTG WDARTYGIPE DT ISQVDPI TLYVLVATVE ALLSAGITDP YEFYKYVHVS EVGNCSGSGM GGVSALRGMF KDRYADKPVQ NDILQESFIN TMS AWVNML LLSSSGPIKT PVGACATAVE SVDIGIETIL SGKAKVVLVG GYDDFQEEGS YEFANMNATS NSIEEFKHGR TPKE MSRPT TTTRNGFMEA QGSGIQVIMT ADLALKMGVP IHAVLAMTAT ATDKIGRSVP APGKGILTTA REHHGNLKYP SPLLN IEYR KRQLNKRLEQ IKSWEETELS YLQEEAELAK EEFGDEFSMH EFLKERTEEV YRESKRQVSD AKKQWGNSFY KSDPRI APL RGALAAFNLT IDDIGVASFH GTSTVANDKN ESATINNMMK HLGRSEGNPV FGVFQKYLTG HPKGAAGAWM LNGAIQI LE SGLVPGNRNA DNVDKLLEQY EYVLYPSRSI QTDGIKAVSV TSFGFGQKGA QAVVVHPDYL FAVLDRSTYE EYATKVSA R NKKTYRYMHN AITRNTMFVA KDKAPYSDEL EQPVYLDPLA RVEENKKKLV FSDKTIQSSQ SYVGEVAQKT AKALSTLNK SSKGVGVDVE LLSAINIDNE TFIERNFTGN EVEYCLNTAH PQASFTGTWS AKEAVFKALG VESKGAGASL IDIEITRDVN GAPKVILHG EAKKAAAKAG VKNVNISISH DDFQATAVAL SEF

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: 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 #3: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAP
Molecular weightTheoretical: 743.405 Da
Chemical component information

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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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

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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
GridPretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2uv8

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 24417
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2) / Details: cryoSPARC2
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)

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Atomic model buiding 1

Initial modelPDB ID:

2uv8


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

PDB-6u5w:
Electron cryomicroscopy structure of C. albicans FAS in the KS-stalled state

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