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Yorodumi- EMDB-13594: Cryo-EM structure of Saccharomyces cerevisiae TOROID (TORC1 Organ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13594 | |||||||||||||||
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Title | Cryo-EM structure of Saccharomyces cerevisiae TOROID (TORC1 Organized in Inhibited Domains). | |||||||||||||||
Map data | Main EM map of TORC1 in TOROID (TORC1 Organized in Inhibited Domains), obtained by Single Particle Analysis (SPA) after signal subtraction performed on TOROID filaments. | |||||||||||||||
Sample |
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Function / homology | Function and homology information PIP3 activates AKT signaling / CD28 dependent PI3K/Akt signaling / regulation of snRNA pseudouridine synthesis / mitochondria-nucleus signaling pathway / Regulation of TP53 Degradation / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / establishment or maintenance of actin cytoskeleton polarity / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation ...PIP3 activates AKT signaling / CD28 dependent PI3K/Akt signaling / regulation of snRNA pseudouridine synthesis / mitochondria-nucleus signaling pathway / Regulation of TP53 Degradation / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / establishment or maintenance of actin cytoskeleton polarity / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / fungal-type cell wall organization / TORC2 complex / Amino acids regulate mTORC1 / TORC1 complex / fungal-type vacuole membrane / vacuolar membrane / negative regulation of macroautophagy / positive regulation of Rho protein signal transduction / positive regulation of endocytosis / TOR signaling / cytoskeleton organization / cellular response to starvation / nuclear periphery / negative regulation of autophagy / response to nutrient / ubiquitin binding / regulation of autophagy / regulation of cell growth / regulation of actin cytoskeleton organization / cellular response to amino acid stimulus / positive regulation of protein serine/threonine kinase activity / cytoplasmic stress granule / ribosome biogenesis / protein-macromolecule adaptor activity / positive regulation of cell growth / endosome membrane / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / phosphorylation / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / signal transduction / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.87 Å | |||||||||||||||
Authors | Felix J / Prouteau M / Bourgoint C / Bonadei L / Desfosses A / Gabus C / Sadian Y / Savvides SN / Gutsche I / Loewith R | |||||||||||||||
Funding support | European Union, 4 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: EGOC inhibits TOROID polymerization by structurally activating TORC1. Authors: Manoël Prouteau / Clélia Bourgoint / Jan Felix / Lenny Bonadei / Yashar Sadian / Caroline Gabus / Savvas N Savvides / Irina Gutsche / Ambroise Desfosses / Robbie Loewith / Abstract: Target of rapamycin complex 1 (TORC1) is a protein kinase controlling cell homeostasis and growth in response to nutrients and stresses. In Saccharomyces cerevisiae, glucose depletion triggers a ...Target of rapamycin complex 1 (TORC1) is a protein kinase controlling cell homeostasis and growth in response to nutrients and stresses. In Saccharomyces cerevisiae, glucose depletion triggers a redistribution of TORC1 from a dispersed localization over the vacuole surface into a large, inactive condensate called TOROID (TORC1 organized in inhibited domains). However, the mechanisms governing this transition have been unclear. Here, we show that acute depletion and repletion of EGO complex (EGOC) activity is sufficient to control TOROID distribution, independently of other nutrient-signaling pathways. The 3.9-Å-resolution structure of TORC1 from TOROID cryo-EM data together with interrogation of key interactions in vivo provide structural insights into TORC1-TORC1' and TORC1-EGOC interaction interfaces. These data support a model in which glucose-dependent activation of EGOC triggers binding to TORC1 at an interface required for TOROID assembly, preventing TORC1 polymerization and promoting release of active TORC1. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13594.map.gz | 91.3 MB | EMDB map data format | |
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Header (meta data) | emd-13594-v30.xml emd-13594.xml | 27.8 KB 27.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13594_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_13594.jpg emd_13594.png | 2.9 MB 157.9 KB | ||
Others | emd_13594_half_map_1.map.gz emd_13594_half_map_2.map.gz | 95.4 MB 95.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13594 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13594 | HTTPS FTP |
-Related structure data
Related structure data | 7pqhMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13594.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Main EM map of TORC1 in TOROID (TORC1 Organized in Inhibited Domains), obtained by Single Particle Analysis (SPA) after signal subtraction performed on TOROID filaments. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: EM half map 1 of TORC1 in TOROID...
File | emd_13594_half_map_1.map | ||||||||||||
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Annotation | EM half map 1 of TORC1 in TOROID (TORC1 Organized in Inhibited Domains), obtained by Single Particle Analysis (SPA) after signal subtraction performed on TOROID filaments. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EM half map 2 of TORC1 in TOROID...
File | emd_13594_half_map_2.map | ||||||||||||
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Annotation | EM half map 2 of TORC1 in TOROID (TORC1 Organized in Inhibited Domains), obtained by Single Particle Analysis (SPA) after signal subtraction performed on TOROID filaments. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TORC1 Organized in Inhibited Domains (TOROID)
Entire | Name: TORC1 Organized in Inhibited Domains (TOROID) |
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Components |
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-Supramolecule #1: TORC1 Organized in Inhibited Domains (TOROID)
Supramolecule | Name: TORC1 Organized in Inhibited Domains (TOROID) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) Strain: RL174-5b: MATa; TB50, KOG1::TAP-HIS3 tor1Delta::KanMX6 |
-Macromolecule #1: Target of rapamycin complex 1 subunit KOG1,Target of rapamycin co...
Macromolecule | Name: Target of rapamycin complex 1 subunit KOG1,Target of rapamycin complex 1 subunit Kog1 type: protein_or_peptide / ID: 1 Details: S. cerevisiae TOROIDS (TORC1 Organized in Inhibited Domains) in the sample are composed of Kog1 (P38873) Lst8, P41318) and Tor2 (P32600),S. cerevisiae TOROIDS (TORC1 Organized in Inhibited ...Details: S. cerevisiae TOROIDS (TORC1 Organized in Inhibited Domains) in the sample are composed of Kog1 (P38873) Lst8, P41318) and Tor2 (P32600),S. cerevisiae TOROIDS (TORC1 Organized in Inhibited Domains) in the sample are composed of Kog1 (P38873) Lst8, P41318) and Tor2 (P32600) Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 183.594562 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MPEIYGPQPL KPLNTVMRHG FEEQYQSDQL LQSLANDFIF YFDDKRHKTN GNPIPEEDKQ RDVNRYYQPI TDWKIMKDRQ KTVSAALLL CLNLGVDPPD VMKTHPCARV EAWVDPLNFQ DSKKAIEQIG KNLQAQYETL SLRTRYKQSL DPCVEDVKRF C NSLRRTSK ...String: MPEIYGPQPL KPLNTVMRHG FEEQYQSDQL LQSLANDFIF YFDDKRHKTN GNPIPEEDKQ RDVNRYYQPI TDWKIMKDRQ KTVSAALLL CLNLGVDPPD VMKTHPCARV EAWVDPLNFQ DSKKAIEQIG KNLQAQYETL SLRTRYKQSL DPCVEDVKRF C NSLRRTSK EDRILFHYNG HGVPKPTKSG EIWVFNRGYT QYIPVSLYDL QTWLGAPCIF VYDCNSAENI LINFQKFVQK RI KDDEEGN HDVAAPSPTS AYQDCFQLAS CTSDELLLMS PELPADLFSC CLTCPIEISI RIFLMQSPLK DSKYKIFFEN STS NQPFGD SKNSFKSKIP NVNIPGMLSD RRTPLGELNW IFTAITDTIA WTSLPRPLFK KLFRHDLMIA ALFRNFLLAK RIMP WYNCH PVSDPELPDS ITTHPMWKSW DLAMDEVLTK IVIDLKNAPP ATALESQMIL QQQETLQNGG SSKSNAQDTK AGSIQ TQSR FAVANLSTMS LVNNPALQSR KSISLQSSQQ QLQQQQQQQQ QFTGFFEQNL TAFELWLKYA SNVRHPPEQL PIVLQV LLS QVHRIRALVL LSRFLDLGPW AVYLSLSIGI FPYVLKLLQS PAPELKPILV FIWARIMSID YKNTQSELIK EKGYMYF VT VLVPDWGVNG MSATNGSAMI NSGNPLTMTA SQNINGPSSR YYERQQGNRT SNLGHNNLPF YHSNDTTDEQ KAMAVFVL A SFVRNFPLGQ KNCFSLELVN KLCFYIDNSE IPLLRQWCVI LLGLLFADNP LNRFVCMNTG AVEILLKSLK DPVPEVRTA SIFALKHFIS GFQDAEVILR LQQEFEEQYQ QLHSQLQHLQ NQSHLQQQQS QQQQQHLEQQ QMKIEKQIRH CQVMQNQLEV IDLRKLKRQ EIGNLISILP LINDGSSLVR KELVVYFSHI VSRYSNFFIV VVFNDLLEEI KLLEKSDINT RNTSDKYSVS Q GSIFYTVW KSLLILAEDP FLENKELSKQ VIDYILLELS AHKELGGPFA VMEKFLLKRS SKAHQTGKFG FNSSQVQFVK SS LRSFSPN ERVDNNAFKK EQQQHDPKIS HPMRTSLAKL FQSLGFSESN SDSDTQSSNT SMKSHTSKKG PSGLYLLNGN NNI YPTAET PRFRKHTEPL QLPLNSSFLD YSREYFQEPQ MKKQEADEPG SVEYNARLWR RNRNETIIQE TQGEKKLSIY GNWS KKLIS LNNKSQPKLM KFAQFEDQLI TADDRSTITV FDWEKGKTLS KFSNGTPFGT KVTDLKLINE DDSALLLTGS SDGVI KIYR DYQDVDTFKI VSAWRGLTDM LLTPRSTGLL TEWLQIRGSL LTTGDVKVIR VWDAHTETVE VDIPAKTSSL ITSLTA DQL AGNIFVAGFA DGSLRVYDRR LDPRDSMIRR WRAGNDKQGV WINNVHLQRG GYRELVSGAT NGVVELWDIR SEDPVES FV DQNVTSQYGS QQKPTTMTCM QVHEHAPIIA TGTKQIKIWT TSGDLLNSFK NSHNNGVTST LAATGIPKSL SYSSTSDA F LSSMAFHPHR MMIAATNSHD SIVNIYKCED ERIDYFRTLQ VDKRRWKKNF IAVSAANRFK KISSSGALDY DIPTTASVD GSENLYFQ |
-Macromolecule #2: Target of rapamycin complex subunit LST8
Macromolecule | Name: Target of rapamycin complex subunit LST8 / type: protein_or_peptide / ID: 2 Details: S. cerevisiae TOROIDs (TORC1 Organized in Inhibited Domains) in the sample are composed of Kog1 (P38873), Lst8 (P41318) and Tor2 (P32600) Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 34.077879 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MSVILVSAGY DHTIRFWEAL TGVCSRTIQH SDSQVNRLEI TNDKKLLATA GHQNVRLYDI RTTNPNPVAS FEGHRGNVTS VSFQQDNRW MVTSSEDGTI KVWDVRSPSI PRNYKHNAPV NEVVIHPNQG ELISCDRDGN IRIWDLGENQ CTHQLTPEDD T SLQSLSMA ...String: MSVILVSAGY DHTIRFWEAL TGVCSRTIQH SDSQVNRLEI TNDKKLLATA GHQNVRLYDI RTTNPNPVAS FEGHRGNVTS VSFQQDNRW MVTSSEDGTI KVWDVRSPSI PRNYKHNAPV NEVVIHPNQG ELISCDRDGN IRIWDLGENQ CTHQLTPEDD T SLQSLSMA SDGSMLAAAN TKGNCYVWEM PNHTDASHLK PVTKFRAHST YITRILLSSD VKHLATCSAD HTARVWSIDD DF KLETTLD GHQRWVWDCA FSADSAYLVT ASSDHYVRLW DLSTREIVRQ YGGHHKGAVC VALNDV |
-Macromolecule #3: Serine/threonine-protein kinase TOR2
Macromolecule | Name: Serine/threonine-protein kinase TOR2 / type: protein_or_peptide / ID: 3 Details: S. cerevisiae TOROIDs (TORC1 Organized in Inhibited Domains) in the sample are composed of Kog1 (P38873), Lst8 (P41318) and Tor2 (P32600) Number of copies: 4 / Enantiomer: LEVO / EC number: 1-phosphatidylinositol 4-kinase |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 281.915438 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MNKYINKYTT PPNLLSLRQR AEGKHRTRKK LTHKSHSHDD EMSTTSNTDS NHNGPNDSGR VITGSAGHIG KISFVDSELD TTFSTLNLI FDKLKSDVPQ ERASGANELS TTLTSLAREV SAEQFQRFSN SLNNKIFELI HGFTSSEKIG GILAVDTLIS F YLSTEELP ...String: MNKYINKYTT PPNLLSLRQR AEGKHRTRKK LTHKSHSHDD EMSTTSNTDS NHNGPNDSGR VITGSAGHIG KISFVDSELD TTFSTLNLI FDKLKSDVPQ ERASGANELS TTLTSLAREV SAEQFQRFSN SLNNKIFELI HGFTSSEKIG GILAVDTLIS F YLSTEELP NQTSRLANYL RVLIPSSDIE VMRLAANTLG RLTVPGGTLT SDFVEFEVRT CIDWLTLTAD NNSSSSKLEY RR HAALLII KALADNSPYL LYPYVNSILD NIWVPLRDAK LIIRLDAAVA LGKCLTIIQD RDPALGKQWF QRLFQGCTHG LSL NTNDSV HATLLVFREL LSLKAPYLRD KYDDIYKSTM KYKEYKFDVI RREVYAILPL LAAFDPAIFT KKYLDRIMVH YLRY LKNID MNAANNSDKP FILVSIGDIA FEVGSSISPY MTLILDNIRE GLRTKFKVRK QFEKDLFYCI GKLACALGPA FAKHL NKDL LNLMLNCPMS DHMQETLMIL NEKIPSLEST VNSRILNLLS ISLSGEKFIQ SNQYDFNNQF SIEKARKSRN QSFMKK TGE SNDDITDAQI LIQCFKMLQL IHHQYSLTEF VRLITISYIE HEDSSVRKLA ALTSCDLFIK DDICKQTSVH ALHSVSE VL SKLLMIAITD PVAEIRLEIL QHLGSNFDPQ LAQPDNLRLL FMALNDEIFG IQLEAIKIIG RLSSVNPAYV VPSLRKTL L ELLTQLKFSN MPKKKEESAT LLCTLINSSD EVAKPYIDPI LDVILPKCQD ASSAVASTAL KVLGELSVVG GKEMTRYLK ELMPLIINTF QDQSNSFKRD AALTTLGQLA ASSGYVVGPL LDYPELLGIL INILKTENNP HIRRGTVRLI GILGALDPYK HREIEVTSN SKSSVEQNAP SIDIALLMQG VSPSNDEYYP TVVIHNLMKI LNDPSLSIHH TAAIQAIMHI FQNLGLRCVS F LDQIIPGI ILVMRSCPPS QLDFYFQQLG SLISIVKQHI RPHVEKIYGV IREFFPIIKL QITIISVIES ISKALEGEFK RF VPETLTF FLDILENDQS NKRIVPIRIL KSLVTFGPNL EDYSHLIMPI VVRMTEYSAG SLKKISIITL GRLAKNINLS EMS SRIVQA LVRILNNGDR ELTKATMNTL SLLLLQLGTD FVVFVPVINK ALLRNRIQHS VYDQLVNKLL NNECLPTNII FDKE NEVPE RKNYEDEMQV TKLPVNQNIL KNAWYCSQQK TKEDWQEWIR RLSIQLLKES PSACLRSCSS LVSVYYPLAR ELFNA SFSS CWVELQTSYQ EDLIQALCKA LSSSENPPEI YQMLLNLVEF MEHDDKPLPI PIHTLGKYAQ KCHAFAKALH YKEVEF LEE PKNSTIEALI SINNQLHQTD SAIGILKHAQ QHNELQLKET WYEKLQRWED ALAAYNEKEA AGEDSVEVMM GKLRSLY AL GEWEELSKLA SEKWGTAKPE VKKAMAPLAA GAAWGLEQWD EIAQYTSVMK SQSPDKEFYD AILCLHRNNF KKAEVHIF N ARDLLVTELS ALVNESYNRA YNVVVRAQII AELEEIIKYK KLPQNSDKRL TMRETWNTRL LGCQKNIDVW QRILRVRSL VIKPKEDAQV RIKFANLCRK SGRMALAKKV LNTLLEETDD PDHPNTAKAS PPVVYAQLKY LWATGLQDEA LKQLINFTSR MAHDLGLDP NNMIAQSVPQ QSKRVPRHVE DYTKLLARCF LKQGEWRVCL QPKWRLSNPD SILGSYLLAT HFDNTWYKAW H NWALANFE VISMLTSVSK KKQEGSDASS VTDINEFDNG MIGVNTFDAK EVHYSSNLIH RHVIPAIKGF FHSISLSESS SL QDALRLL TLWFTFGGIP EATQAMHEGF NLIQIGTWLE VLPQLISRIH QPNQIVSRSL LSLLSDLGKA HPQALVYPLM VAI KSESLS RQKAALSIIE KMRIHSPVLV DQAELVSHEL IRMAVLWHEQ WYEGLDDASR QFFGEHNTEK MFAALEPLYE MLKR GPETL REISFQNSFG RDLNDAYEWL MNYKKSKDVS NLNQAWDIYY NVFRKIGKQL PQLQTLELQH VSPKLLSAHD LELAV PGTR ASGGKPIVKI SKFEPVFSVI SSKQRPRKFC IKGSDGKDYK YVLKGHEDIR QDSLVMQLFG LVNTLLQNDA ECFRRH LDI QQYPAIPLSP KSGLLGWVPN SDTFHVLIRE HREAKKIPLN IEHWVMLQMA PDYDNLTLLQ KVEVFTYALN NTEGQDL YK VLWLKSRSSE TWLERRTTYT RSLAVMSMTG YILGLGDRHP SNLMLDRITG KVIHIDFGDC FEAAILREKF PEKVPFRL T RMLTYAMEVS GIEGSFRITC ENVMKVLRDN KGSLMAILEA FAFDPLINWG FDLPTKKIEE ETGIQLPVMN ANELLSNGA ITEEEVQRVE NEHKNAIRNA RAMLVLKRIT DKLTGNDIRR FNDLDVPEQV DKLIQQATSV ENLCQHYIGW CPFW |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.02 mg/mL | ||||||||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 37000 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-16 / Number real images: 4901 / Average exposure time: 8.0 sec. / Average electron dose: 20.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Details | Initial homology models of Tor2 and Lst8 were generated using Phyre2, while a model of Kog1 was generated using ITasser. Homology models of Tor2, Lst8 and Kog1 were first manually placed in the final 3D map followed by rigid-body fitting in Chimera. The rigid-body fitted models were subsequently subjected to a round of flexible fitting using Imodfit followed by automatic molecular dynamics flexible fitting using NAMDINATOR. The flexibly fitted structure was then refined using the Phenix software package. |
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Refinement | Protocol: OTHER |
Output model | PDB-7pqh: |