[English] 日本語
Yorodumi- EMDB-13846: Protein community member fatty acid synthase complex from C. ther... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13846 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Protein community member fatty acid synthase complex from C. thermophilum | |||||||||
Map data | Protein community member C. thermophilum Fatty Acid Synthase | |||||||||
Sample |
| |||||||||
Keywords | Fatty 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 / long-chain fatty acid biosynthetic process / fatty acid synthase activity / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.47 Å | |||||||||
Authors | Skalidis I / Kyrilis FL / Tueting C / Hamdi F / Kastritis PL | |||||||||
Funding support | 1 items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13846.map.gz | 59.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-13846-v30.xml emd-13846.xml | 23.9 KB 23.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13846_fsc.xml | 8.9 KB | Display | FSC data file |
Images | emd_13846.png | 84.7 KB | ||
Masks | emd_13846_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-13846.cif.gz | 8.2 KB | ||
Others | emd_13846_additional_1.map.gz emd_13846_half_map_1.map.gz emd_13846_half_map_2.map.gz | 117.1 MB 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13846 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13846 | HTTPS FTP |
-Related structure data
Related structure data | 7q5sMC 7q5qC 7q5rC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10892 (Title: Cryo-EM SPA dataset of Megadalton-range protein communities from a Chaetomium thermophilum native cell extract Data size: 1.1 TB Data #1: Unaligned fractions saved by Falcon 3 EC camera [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_13846.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Protein community member C. thermophilum Fatty Acid Synthase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.5678 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_13846_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Protein community member C. thermophilum Signature 3 Ab Initio Map
File | emd_13846_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Protein community member C. thermophilum Signature 3 Ab Initio Map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Protein community member C. thermophilum Fatty Acid Synthase,...
File | emd_13846_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Protein community member C. thermophilum Fatty Acid Synthase, Half-Map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Protein community member C. thermophilum Fatty Acid Synthase,...
File | emd_13846_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Protein community member C. thermophilum Fatty Acid Synthase, Half-Map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Fatty Acid Synthase Complex from Chaetomium thermophilum
Entire | Name: Fatty Acid Synthase Complex from Chaetomium thermophilum |
---|---|
Components |
|
-Supramolecule #1: Fatty Acid Synthase Complex from Chaetomium thermophilum
Supramolecule | Name: 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) |
-Macromolecule #1: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
Macromolecule | Name: 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 weight | Theoretical: 235.450672 KDa |
Sequence | String: 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 |
-Macromolecule #2: 3-oxoacyl-[acyl-carrier-protein] reductase
Macromolecule | Name: 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 weight | Theoretical: 205.066922 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
---|---|
Buffer | pH: 7.4 / Component - Concentration: 200.0 mM / Component - Formula: NH4CH2COOH / Component - Name: Ammonium acetate |
Vitrification | Cryogen 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.. |
-Electron microscopy
Microscope | TFS GLACIOS |
---|---|
Temperature | Min: 77.15 K / Max: 103.15 K |
Alignment procedure | Coma free - Residual tilt: 14.7 mrad |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 2808 / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 95675 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 92000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Details | Initial 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 |
---|---|
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-7q5s: |