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- EMDB-13846: Protein community member fatty acid synthase complex from C. ther... -

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Basic information

Entry
Database: EMDB / ID: EMD-13846
TitleProtein community member fatty acid synthase complex from C. thermophilum
Map dataProtein community member C. thermophilum Fatty Acid Synthase
Sample
  • Complex: Fatty Acid Synthase Complex from Chaetomium thermophilum
    • Protein or peptide: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
    • Protein or peptide: 3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsFatty Acid Synthase / complex / chaetomium / thermophilum / fatty / acid / synthesis / TRANSFERASE
Function / homology
Function and homology information


fatty acid synthase complex / holo-[acyl-carrier-protein] synthase activity / fatty acid synthase activity / long-chain fatty acid biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / magnesium ion binding
Similarity search - Function
: / Fatty acid synthase beta subunit AflB /Fas1-like, fungi / 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 / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain ...: / Fatty acid synthase beta subunit AflB /Fas1-like, fungi / 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 / 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 / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 alpha subunit-like protein / Malonyltransferase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.47 Å
AuthorsSkalidis I / Kyrilis FL / Tueting C / Hamdi F / Kastritis PL
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2022
Title: Cryo-EM and artificial intelligence visualize endogenous protein community members.
Authors: Ioannis Skalidis / Fotis L Kyrilis / Christian Tüting / Farzad Hamdi / Grzegorz Chojnowski / Panagiotis L Kastritis /
Abstract: Cellular function is underlined by megadalton assemblies organizing in proximity, forming communities. Metabolons are protein communities involving metabolic pathways such as protein, fatty acid, and ...Cellular function is underlined by megadalton assemblies organizing in proximity, forming communities. Metabolons are protein communities involving metabolic pathways such as protein, fatty acid, and thioesters of coenzyme-A synthesis. Metabolons are highly heterogeneous due to their function, making their analysis particularly challenging. Here, we simultaneously characterize metabolon-embedded architectures of a 60S pre-ribosome, fatty acid synthase, and pyruvate/oxoglutarate dehydrogenase complex E2 cores de novo. Cryo-electron microscopy (cryo-EM) 3D reconstructions are resolved at 3.84-4.52 Å resolution by collecting <3,000 micrographs of a single cellular fraction. After combining cryo-EM with artificial intelligence-based atomic modeling and de novo sequence identification methods, at this resolution range, polypeptide hydrogen bonding patterns are discernible. Residing molecular components resemble their purified counterparts from other eukaryotes but also exhibit substantial conformational variation with potential functional implications. Our results propose an integrated tool, boosted by machine learning, that opens doors for structural systems biology spearheaded by cryo-EM characterization of native cell extracts.
History
DepositionNov 4, 2021-
Header (metadata) releaseFeb 2, 2022-
Map releaseFeb 2, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7q5s
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7q5s
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13846.png

Downloads & links

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Map

FileDownload / File: emd_13846.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationProtein community member C. thermophilum Fatty Acid Synthase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.57 Å/pix.
x 256 pix.
= 401.357 Å		1.57 Å/pix.
x 256 pix.
= 401.357 Å		1.57 Å/pix.
x 256 pix.
= 401.357 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5678 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-1.0015457 - 2.8023229
Average (Standard dev.)0.0072308765 (±0.24349988)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 401.3568 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.567800781251.567800781251.56780078125
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z401.357401.357401.357
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.0022.8020.007

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Supplemental data

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Mask #1

Fileemd_13846_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Protein community member C. thermophilum Signature 3 Ab Initio Map

Fileemd_13846_additional_1.map
AnnotationProtein community member C. thermophilum Signature 3 Ab Initio Map
Projections & Slices
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Half map: Protein community member C. thermophilum Fatty Acid Synthase,...

Fileemd_13846_half_map_1.map
AnnotationProtein community member C. thermophilum Fatty Acid Synthase, Half-Map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Protein community member C. thermophilum Fatty Acid Synthase,...

Fileemd_13846_half_map_2.map
AnnotationProtein community member C. thermophilum Fatty Acid Synthase, Half-Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Fatty Acid Synthase Complex from Chaetomium thermophilum

EntireName: Fatty Acid Synthase Complex from Chaetomium thermophilum
Components
  • Complex: Fatty Acid Synthase Complex from Chaetomium thermophilum
    • Protein or peptide: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
    • Protein or peptide: 3-oxoacyl-[acyl-carrier-protein] reductase

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Supramolecule #1: Fatty Acid Synthase Complex from Chaetomium thermophilum

SupramoleculeName: Fatty Acid Synthase Complex from Chaetomium thermophilum
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)

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Macromolecule #1: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase

MacromoleculeName: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Molecular weightTheoretical: 235.450672 KDa
SequenceString: MYGTGTGPQT GAVTPRSSAS LRPLTLSHGS LETSFLIPTG LHFHASRLKD EFIASLPPPT DELAQDDEPS SVPELVARYM GYIANQVAE GEDDAQGSYE EVLKLILNEF ERAFLQGNDV HALVATLPGI DAKKLEVIRS YFAARAATNR AMRAHQSALL R AAEEGEAR ...String:
MYGTGTGPQT GAVTPRSSAS LRPLTLSHGS LETSFLIPTG LHFHASRLKD EFIASLPPPT DELAQDDEPS SVPELVARYM GYIANQVAE GEDDAQGSYE EVLKLILNEF ERAFLQGNDV HALVATLPGI DAKKLEVIRS YFAARAATNR AMRAHQSALL R AAEEGEAR IYSIFGGQGN IEEYFEELRE LYKTYPSFVG HLIVSSAELL QILASHPSAE KLYSKGLDIM HWLHNPDATP DT DYLISAP VSFPLIGLVQ LAHYQVTCKV QGLHPGILRD RISGTTGHSQ GIVLAAVTAA ADSWESFEDL AKSALTILFW IGA RSQQTF PRTSMSPSLL QEAIDNGEGT PTPMLSIRDL PQAEVQKHID QTNQYLPEDQ HISISLINSP RNLVVSGPPR SLCG LNAQL RKVKAPTGLD QARIPYSERK IRFVNRFLPI TAPFHSKYLA GAAELIAEDL KDISIEVERL GIPVYDTNTG EDIRQ TVTG NVVPALIRMI TNDPVHWEKA TVFPEATHIL DFGPGGISGL GVLTSRNKDG TGVRVILAGT VNGTVAEVGY KSELFD RDE EHAVKYAVDW VKEYGPRLIK TSSGRIYVDT KMSRLLGLPP LMVAGMTPTT VPWDFVAATM NAGYQIELAG GGYFNAK MM TEAISKIERA IPPGRGITVN LIYVNPHAMA WQIPLLGRLR AEGVPIEGLT IGAGVPSIEV ANEYIQTLGL KHISFKPG S VDAIQAVINI AKANPTFPVI LQWTGGRGGG HHSYEDFHAP ILAMYSRIRR QENIILVAGS GFGGAEDTYP YLTGAWSTK YGYPPMPFDG CLFGSRMMVA KEAHTSPEAK QAIVDAPGLD DSEWEKTYKG PAGGVITVRS EMGEPIHKLA TRGVLFWAEM DQKIFSLPK EKRVAELKKN RDYIIRKLNA DFQKVWFGKN KKGEVVDLED MTYGEVVRRM VELLYVKDEK RWIDHSFAKL T ADFIHRVE ERFTTAASQP SLIQSYSDLD EPYSAVERVL AHYPEAETQL ISAQDVQHFL LLCKRRGQKP VTFVPALDED FE FYFKKDS LWQSEDLAAV IDRDVGRTCI LQGPMAAKHS TKVDEPIKEI LDGIHNGHIA ALKRDLYDND ESKIPTIEYF GGK LKDPEV QLDFEGVTIS YDVHKNTYRV SNNPSVPLPP LDAWLSALAG PNRTWRYALL QSEVIVQGHK YQTNPMKKIF APAR GLFVE IQYPNDPAKT VITVKEQPRP NRYIDVIEAK LVGDKEIVVN LIKDTNALGE PVALPLRFTY RPEAGYAPIH EIMEG RNDR IKEFYWRCWF GQDPLDLDAP VTSKFDGGEA VITSEAINEF VHAVGNTGEA FVDRPGKTMY APMDFAIVVG WKAITK PIF PRTIDGDLLK LVHLSNQFRM FPGAEPLKKG DKVYTTAQVN AVINQESGKM VEVCGTITRD GKPVMEVISQ FLYRGVY TD YENTFQRKVE TPMQVHLATT KDIAILRSKQ WFVLDDVATP EEFLLGKTLT FRLHTLVHFK NRNVYSHVET RGQVLVEL P TKEIIQVATV EYVAGESHGN PVIDYLQRNG QSIEQPVNFE NPIPLGGKAP LQLRAPASNE TYARVSGDYN PIHVSRVFA AYANLPGTIT HGMYSSAAVR SLVETWAAEN KIGRVRSFHA SLTGMVLPND DINVKLQHVG MVGGRKIIKV EATNKETEEK VLLGEAEIE QPVTAYVFTG QGSQEQGMGM DLYANSPVAR EVWDRADKYL RDTYGFAITD IVRNNPKELT IHFGGPLGKK I RANYMAMT FETVAADGSI KSERIFKDID ENTTSYTFRS PNGLLSATQF TQPALTLMEK ASFEDMKAKG LVPRDSTFAG HS LGEYSAL AALADVMPIE SLVSVVFYRG LTMQVAVERD ATGRSNYGMC AVNPSRISKT FNEEALRFVV GAVAETTGWL LEI VNYNIA NMQYVCAGDL RALDTLTSVT NFIKAMKIDI EQMRREYSPD KVKEELVEII KKCAAETEAK PKPLELQRGF ATIP LRGID VPFHSTFLRS GVKPFRNFLL KKINKTSIDP AKLIGKYIPN VTAKPFALTK EYFEDVYRLT NSPRIAHVLA NWEKY QDDN STLSASVANT SSETNGVNGV NGAVDVNGQN GVNGVNGH

UniProtKB: Malonyltransferase-like protein

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Macromolecule #2: 3-oxoacyl-[acyl-carrier-protein] reductase

MacromoleculeName: 3-oxoacyl-[acyl-carrier-protein] reductase / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Molecular weightTheoretical: 205.066922 KDa
SequenceString: MRPEVEQELA HTLLVELLAY QFASPVRWIE TQDVFLAEQM AERIVEIGPA DTLSVMAKRT LASKYEAYDA AKSAQRQILC YSKDAKEIY YDVDPIEEEP EPAPAQAATP TAPAAPAATP AAAPAPVAAP PPPGVGPAAQ VPDAPVTALE IVRALIAQKL K KPYQEVPL ...String:
MRPEVEQELA HTLLVELLAY QFASPVRWIE TQDVFLAEQM AERIVEIGPA DTLSVMAKRT LASKYEAYDA AKSAQRQILC YSKDAKEIY YDVDPIEEEP EPAPAQAATP TAPAAPAATP AAAPAPVAAP PPPGVGPAAQ VPDAPVTALE IVRALIAQKL K KPYQEVPL SKAIKDLVGG KSTLQNEILG DLGKEFGSTP EKPEDTPLDE LGAAMQATFD GNLGKTSQGL IARLISSKMP GG FNITTAR KYLETRWGLG PGRQDGVLLL AITMEPPSRL GSEADAKAFL DDVSQKYAAN AGISLSTAAA AGPAAGAGGG MLM DPAALE ALTSDQKALF KQQLELIARY LKLDIRAGDK AYQASQESAK VLQSQLDLWL AEHGDFYASG IEPVFSPLKA RVYD SSWNW ARQDALSMYY DIIFGRLKTV DREIVSQCIR IMNRANPTLL EFMQYHIDNC PTDRGETYQL AKELGAQLIE NCKEV LNAN PVYKDVAIPT GPKTTIDARG NLKYEEVPRP SCRKLEHYVQ QMAAGGKISE YGNRIKVQND LAKIYKLIKQ QHKLPK TSQ LEIKALYSDI IRALQMNENQ ILGQTNGKSL GLPKKGKPKA KTETIPFLHL RKKSVMGWEY NKKLTSLYLD CLEKAAR DG LTFAGKYALM TGAGAGSIGA EVLQGLISGG AHVIVTTSRY SREVTEYYQS MYSRYGARGS QLVVVPFNQG SVQDVNAL V EYIYDTKNGL GWDLDYIVPF AAISEQGRQI DGIDSKSELA HRIMLTNLIR LLGAVKTQKA SRGYETRPAQ VILPLSPNH GTFGSDGLYS ESKLGLETLF NRWESENWSN YLTICGAIIG WTRGTGLMSG NNIVAEAVEK FGVRTFSQQE MAFNLLGLMA PTIVDLCQN EPVCADLNGG LQFIPNLNEL MTRERKNLTE TSEIRQAVTK ETAAENKVVN GEASEALYKK KIIERRANIK F DFPPLPDW KKDIQPLNDK LKGMVDLEKV IVVTGFAEVG PWGNSRTRWE MEAYGEFSLE GCIEMAWIMG LIKNYNGLIK GK PYSGWVD AKTGEPVDDK DVKPKYEKYI LEHSGIRLIE PELFGGYDPN KKQLLHEVVI QEDLDPFQCS AETAEQFKRE HGD KVEIFE IPESGEYTVR FKKGATLWIP KALRFDRLVA GQIPTGWDAK RYGIPDDIIQ QVDPVCLFVL VSTVEALLSS GITD PYEFY KYVHVSELGN CIGSGMGGAT ALRGMHRDRF LDKPLQNDIL QESFINTMSA WVNMLLLSSS GPIKTPVAAC ATAVE SVDV GVETILEGKA RICLVGGFDD FGEEGSYEFA NMKATSNAVD EFAHGRTPQE MSRPTTTTRN GFMESQGSGV QVIMTA KLA LEMGVPIYGI LALTTTASDK IGRSVPAPGQ GVLTTAREHR GKFPSPLLDI NYRRRQIERR TKQVMEEKEA EFEYLAA EI EALKAEGRPQ SEIEEYAAHR AAHIEKTAEK QAKEILRSFG NFFWKNDPTI APLRGALAVW GLTIDDLDVA SFHGTSTK A NDKNESSVIC QQLAHLGRKK GNAVLGIFQK YLTGHPKGAA GAWMLNGCLQ VLNTGLVPGN RNADNVDKVM EQFDYIVYP NRSIQTDGIK AFSVTSFGFG QKGAQCIGVH PKYLYATLDE QTYNEYCTKV QARQKKAYRY FHNGLINNTL FQAKEKAPYT DEQLSAVLL NPDARVVEDK KTGQLIFPPN FMKLSEKTQA AAQPKVSLES VLSREARRLE SVNTRVGVDV EDISAINTDN D TFLDRNFT EAEQKYCLAS KSGRSPQKAF AGRWTAKEAV FKALGVSSKG AGAALKDIEI LVDENGAPTV SLHGAAAEAA KK AGIKSVS VSISYTDSQA AAIATAQL

UniProtKB: Fatty acid synthase alpha subunit-like protein

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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

Concentration0.3 mg/mL
BufferpH: 7.4 / Component - Concentration: 200.0 mM / Component - Formula: NH4CH2COOH / Component - Name: Ammonium acetate
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: For plunging, blot force 2 and blotting time of 6 sec were applied..

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 95675 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 92000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
TemperatureMin: 77.15 K / Max: 103.15 K
Alignment procedureComa free - Residual tilt: 14.7 mrad
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 2808 / Average electron dose: 30.0 e/Å2

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1) / Software - details: Ab-Initio Reconstruction
Final 3D classificationNumber classes: 256 / Software - Name: cryoSPARC (ver. 3.1) / Software - details: 2D Classification
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 4.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Software - details: Homogeneous Refinement / Number images used: 5231
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsInitial models were predicted using AlphaFold v2.0.1, fitted into reconstructions using COOT and finally refined in real space using COOT and phenix.real_space_refine
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7q5s:
Protein community member fatty acid synthase complex from C. thermophilum

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