[English] 日本語
Yorodumi
- EMDB-13594: Cryo-EM structure of Saccharomyces cerevisiae TOROID (TORC1 Organ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13594
TitleCryo-EM structure of Saccharomyces cerevisiae TOROID (TORC1 Organized in Inhibited Domains).
Map dataMain 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
  • Complex: TORC1 Organized in Inhibited Domains (TOROID)
    • Protein or peptide: Target of rapamycin complex 1 subunit KOG1,Target of rapamycin complex 1 subunit Kog1
    • Protein or peptide: Target of rapamycin complex subunit LST8MTOR
    • Protein or peptide: Serine/threonine-protein kinase TOR2
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 / positive regulation of Rho guanyl-nucleotide exchange factor activity / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / establishment or maintenance of actin cytoskeleton polarity / VEGFR2 mediated vascular permeability ...PIP3 activates AKT signaling / CD28 dependent PI3K/Akt signaling / regulation of snRNA pseudouridine synthesis / mitochondria-nucleus signaling pathway / Regulation of TP53 Degradation / positive regulation of Rho guanyl-nucleotide exchange factor activity / 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 / positive regulation of Rho protein signal transduction / negative regulation of macroautophagy / positive regulation of endocytosis / TOR signaling / cytoskeleton organization / cellular response to starvation / nuclear periphery / response to nutrient / negative regulation of autophagy / 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 / protein-macromolecule adaptor activity / ribosome biogenesis / positive regulation of cell growth / endosome membrane / regulation of cell cycle / non-specific serine/threonine protein kinase / cell cycle / Golgi membrane / protein phosphorylation / 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
Raptor, N-terminal CASPase-like domain / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / Target of rapamycin complex subunit LST8 / Domain of unknown function DUF3385, target of rapamycin protein / Domain of unknown function (DUF3385) / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR ...Raptor, N-terminal CASPase-like domain / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / Target of rapamycin complex subunit LST8 / Domain of unknown function DUF3385, target of rapamycin protein / Domain of unknown function (DUF3385) / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / HEAT repeat / HEAT repeat / PIK-related kinase, FAT / FAT domain / FATC domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase TOR2 / Target of rapamycin complex 1 subunit KOG1 / Target of rapamycin complex subunit LST8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsFelix J / Prouteau M / Bourgoint C / Bonadei L / Desfosses A / Gabus C / Sadian Y / Savvides SN / Gutsche I / Loewith R
Funding supportEuropean Union, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)834394European Union
Swiss National Science Foundation179517European Union
H2020 Marie Curie Actions of the European Commission789385European Union
European Research Council (ERC)64778European Union
CitationJournal: 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
DepositionSep 17, 2021-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateMar 29, 2023-
Current statusMar 29, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_13594.jpg

emd_13594.png

Downloads & links

-
Map

FileDownload / File: emd_13594.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain 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 sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.057120483 - 2.3437147
Average (Standard dev.)0.0039005666 (±0.04260644)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 405.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: EM half map 1 of TORC1 in TOROID...

Fileemd_13594_half_map_1.map
AnnotationEM 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
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: EM half map 2 of TORC1 in TOROID...

Fileemd_13594_half_map_2.map
AnnotationEM 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
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : TORC1 Organized in Inhibited Domains (TOROID)

EntireName: TORC1 Organized in Inhibited Domains (TOROID)
Components
  • Complex: TORC1 Organized in Inhibited Domains (TOROID)
    • Protein or peptide: Target of rapamycin complex 1 subunit KOG1,Target of rapamycin complex 1 subunit Kog1
    • Protein or peptide: Target of rapamycin complex subunit LST8MTOR
    • Protein or peptide: Serine/threonine-protein kinase TOR2

-
Supramolecule #1: TORC1 Organized in Inhibited Domains (TOROID)

SupramoleculeName: TORC1 Organized in Inhibited Domains (TOROID) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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...

MacromoleculeName: 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
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 183.594562 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: 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

MacromoleculeName: 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
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 34.077879 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: 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

MacromoleculeName: 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
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 281.915438 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: 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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.02 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMMES-NaOH2-(N-morpholino)ethanesulfonic acid-sodium hydroxide
5.0 mMCHAPS3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate
600.0 mMNaClSodium chloridesodium chloride
0.5 mMDTTDithiothreitol
Phosphatase Inhibitor Mix
1.0 1 tablet/50 mlComplete Complete Protease Inhibitor Cocktail (Roche)
1.0 mMPMSFphenylmethylsulfonyl fluoridePMSF
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 recordingFilm 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

Particle selectionNumber selected: 219455
Startup modelType of model: EMDB MAP
EMDB ID:

3814

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.01)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.01)
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.01)
Details: Based on an initial helical reconstruction in RELION2.0, we performed signal subtraction to generate a set of 219,455 subtracted particles containing one isolated Torc1 assembly per segment. ...Details: Based on an initial helical reconstruction in RELION2.0, we performed signal subtraction to generate a set of 219,455 subtracted particles containing one isolated Torc1 assembly per segment. Next, we employed the localrec module in Scipion to crop and re-center the signal subtracted particles in a smaller box of 300 pixels, as well as assigning to each particle a refined defocus based on the helical geometry. Single-particle analysis of the subtracted particles using 3D refinement in RELION2.0, while imposing D1 symmetry, resulted in a map with a resolution of 4.5 Angstrom (FSC = 0.143). We then imported the particles from the RELION2.0 refinement in cryoSPARC 3.01. After 2D classification and class selection, a set of 213808 selected particles was used for Non-Uniform refinement in cryoSPARC 3.01, employing a dynamic mask, imposing D1 symmetry, using the option to keep particles from the same helix in the same half-set, and allowing high-order aberration estimation and correction, which resulted in a final map with a resolution of 3.87 Angstrom (FSC = 0.143).
Number images used: 218872
FSC plot (resolution estimation)

-
Atomic model buiding 1

DetailsInitial 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.
RefinementProtocol: OTHER
Output model

PDB-7pqh:
Cryo-EM structure of Saccharomyces cerevisiae TOROID (TORC1 Organized in Inhibited Domains).

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more