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- EMDB-3896: Cryo-EM Structure of Saccharomyces cerevisiae Target of Rapamycin... -

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Basic information

Entry
Database: EMDB / ID: EMD-3896
TitleCryo-EM Structure of Saccharomyces cerevisiae Target of Rapamycin Complex 2
Map datarefined and postprocessed map
Sample
  • Complex: Target of rapamycin protein complex 2MTOR
    • Protein or peptide: Serine/threonine-protein kinase TOR2
    • Protein or peptide: Target of rapamycin complex subunit LST8MTOR
    • Protein or peptide: Target of rapamycin complex 2 subunit TSC11
    • Protein or peptide: Target of rapamycin complex 2 subunit AVO2
    • Protein or peptide: Target of rapamycin complex 2 subunit AVO1
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 / TORC2 signaling / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / establishment or maintenance of actin cytoskeleton polarity ...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 / TORC2 signaling / 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 / phosphatidylinositol-4,5-bisphosphate binding / nuclear periphery / negative regulation of autophagy / response to nutrient / regulation of cell growth / regulation of actin cytoskeleton organization / ribosome biogenesis / 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
TORC2 component Sin1/Avo1 / SAPK-interacting protein 1, Pleckstrin-homology domain / Sin1, middle CRIM domain / SAPK-interacting protein 1 (Sin1), middle CRIM domain / SAPK-interacting protein 1 (Sin1), Pleckstrin-homology / Target of rapamycin complex subunit LST8 / Domain of unknown function DUF3447 / Domain of unknown function DUF3385, target of rapamycin protein / Domain of unknown function (DUF3385) / Domain of unknown function ...TORC2 component Sin1/Avo1 / SAPK-interacting protein 1, Pleckstrin-homology domain / Sin1, middle CRIM domain / SAPK-interacting protein 1 (Sin1), middle CRIM domain / SAPK-interacting protein 1 (Sin1), Pleckstrin-homology / Target of rapamycin complex subunit LST8 / Domain of unknown function DUF3447 / 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 / 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 / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / PH-like 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 subunit LST8 / Target of rapamycin complex 2 subunit AVO2 / Target of rapamycin complex 2 subunit AVO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsKaruppasamy M / Kusmider B / Oliveira TM / Gaubitz C / Prouteau M / Loewith R / Schaffitzel C
Funding support4 items
OrganizationGrant numberCountry
Swiss National Science FoundationFNS 31003A_160023
European Research CouncilTORCH 614552
Sinergia grantCRSII3_136254
European Research CouncilStarting Grant, No 281331
CitationJournal: Mol Cell / Year: 2015
Title: Molecular Basis of the Rapamycin Insensitivity of Target Of Rapamycin Complex 2.
Authors: Christl Gaubitz / Taiana M Oliveira / Manoel Prouteau / Alexander Leitner / Manikandan Karuppasamy / Georgia Konstantinidou / Delphine Rispal / Sandra Eltschinger / Graham C Robinson / ...Authors: Christl Gaubitz / Taiana M Oliveira / Manoel Prouteau / Alexander Leitner / Manikandan Karuppasamy / Georgia Konstantinidou / Delphine Rispal / Sandra Eltschinger / Graham C Robinson / Stéphane Thore / Ruedi Aebersold / Christiane Schaffitzel / Robbie Loewith /
Abstract: Target of Rapamycin (TOR) plays central roles in the regulation of eukaryote growth as the hub of two essential multiprotein complexes: TORC1, which is rapamycin-sensitive, and the lesser ...Target of Rapamycin (TOR) plays central roles in the regulation of eukaryote growth as the hub of two essential multiprotein complexes: TORC1, which is rapamycin-sensitive, and the lesser characterized TORC2, which is not. TORC2 is a key regulator of lipid biosynthesis and Akt-mediated survival signaling. In spite of its importance, its structure and the molecular basis of its rapamycin insensitivity are unknown. Using crosslinking-mass spectrometry and electron microscopy, we determined the architecture of TORC2. TORC2 displays a rhomboid shape with pseudo-2-fold symmetry and a prominent central cavity. Our data indicate that the C-terminal part of Avo3, a subunit unique to TORC2, is close to the FKBP12-rapamycin-binding domain of Tor2. Removal of this sequence generated a FKBP12-rapamycin-sensitive TORC2 variant, which provides a powerful tool for deciphering TORC2 function in vivo. Using this variant, we demonstrate a role for TORC2 in G2/M cell-cycle progression.
History
DepositionOct 2, 2017-
Header (metadata) releaseOct 18, 2017-
Map releaseDec 6, 2017-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0147
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0147
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6emk
  • Surface level: 0.0147
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6emk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3896.png

Downloads & links

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Map

FileDownload / File: emd_3896.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrefined and postprocessed map
Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 0.0147 / Movie #1: 0.0147
Minimum - Maximum-0.043736793 - 0.10092282
Average (Standard dev.)0.0011989143 (±0.0065768785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 441.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z441.600441.600441.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0440.1010.001

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Supplemental data

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Sample components

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Entire : Target of rapamycin protein complex 2

EntireName: Target of rapamycin protein complex 2MTOR
Components
  • Complex: Target of rapamycin protein complex 2MTOR
    • Protein or peptide: Serine/threonine-protein kinase TOR2
    • Protein or peptide: Target of rapamycin complex subunit LST8MTOR
    • Protein or peptide: Target of rapamycin complex 2 subunit TSC11
    • Protein or peptide: Target of rapamycin complex 2 subunit AVO2
    • Protein or peptide: Target of rapamycin complex 2 subunit AVO1

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Supramolecule #1: Target of rapamycin protein complex 2

SupramoleculeName: Target of rapamycin protein complex 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.4 MDa

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Macromolecule #1: Serine/threonine-protein kinase TOR2

MacromoleculeName: Serine/threonine-protein kinase TOR2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: 1-phosphatidylinositol 4-kinase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
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

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Macromolecule #2: Target of rapamycin complex subunit LST8

MacromoleculeName: Target of rapamycin complex subunit LST8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
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

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Macromolecule #3: Target of rapamycin complex 2 subunit TSC11

MacromoleculeName: Target of rapamycin complex 2 subunit TSC11 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 25.804662 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

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Macromolecule #4: Target of rapamycin complex 2 subunit AVO2

MacromoleculeName: Target of rapamycin complex 2 subunit AVO2 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 47.206457 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MLKEPSVRLR EAIIEGNLLI VKRLLRRNPD LLTNIDSENG WSSLHYASYH GRYLICVYLI QLGHDKHELI KTFKGNTCVH LALMKGHEQ TLHLLLQQFP RFINHRGENG RAPIHIACMN DYYQCLSLLI GVGADLWVMD TNGDTPLHVC LEYGSISCMK M LLNEGEVS ...String:
MLKEPSVRLR EAIIEGNLLI VKRLLRRNPD LLTNIDSENG WSSLHYASYH GRYLICVYLI QLGHDKHELI KTFKGNTCVH LALMKGHEQ TLHLLLQQFP RFINHRGENG RAPIHIACMN DYYQCLSLLI GVGADLWVMD TNGDTPLHVC LEYGSISCMK M LLNEGEVS LDDNVRDKGN WKPIDVAQTF EVGNIYSKVL KEVKKKGPPL GAGKKPSSFR TPILNAKATF EDGPSPVLSM NS PYSLYSN NSPLPVLPRR ISTHTTSGNG GNRRSSITNP VFNPRKPTLS TDSFSSSSNS SSRLRVNSIN VKTPVGVSPK KEL VSESVR HSATPTSPHN NIALINRYLL PNKSNDNVRG DSQTATINDD GGGGNGGDAT IGMGLRKDPD DENENKYKIK VNNG EPRRR VSLLNIPISK LRNSNNTRAE D

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Macromolecule #5: Target of rapamycin complex 2 subunit AVO1

MacromoleculeName: Target of rapamycin complex 2 subunit AVO1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 131.565453 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDTVTVLNEL RAQFLRVCPE KDQMKRIIKP YIPVDEFNTE QCLDSSIREL YMNSDGVSLL PELESPPVSK DFMENYASLG KMRIMRENE GQKGKANQNL IGAEKTERDE EETRNLQDKS AKNTLIVEEN GTLRYNPLNS SASNSLLNDD DHTSGKHHKT S SKEDSYLN ...String:
MDTVTVLNEL RAQFLRVCPE KDQMKRIIKP YIPVDEFNTE QCLDSSIREL YMNSDGVSLL PELESPPVSK DFMENYASLG KMRIMRENE GQKGKANQNL IGAEKTERDE EETRNLQDKS AKNTLIVEEN GTLRYNPLNS SASNSLLNDD DHTSGKHHKT S SKEDSYLN SSMEMQKKSS KRSSLPFVRI FKSRRDHSNT SGNKNVMNTT NTRAKSSTLH PPGARHNKKG SKFDMNFDFD EN LEEEDDD DDDDEEGDDI HSQFFQLDDD FDAKGSGASP AHKGINGMSN NKNNTYTNNR NSISILDDRE SSNGNIGSAS RLK SHFPTS QKGKIFLTDN KNDGQKSDSL NANKGIHGDG SSASGNGSVS RDGLTETESN NISDMESYIN EKDLDDLNFD TVTS NINKT VSDLGGHEST NDGTAVMNRD SKDSRSNSNE FNAQNRDRIT PGSSYGKSLL GSEYSEERYS NNDSSTMESG EMSLD SDMQ TNTIPSHSIP MSMQKYGIYH GDDDSTLNNV FDKAVLTMNS SRHPKERRDT VISGKEPTSL TSSNRKFSVS SNLTST RSP LLRGHGRTSS TASSEHMKAP KVSDSVLHRA RKSTLTLKQD HSQPSVPSSV HKSSKEGNIL IEKTTDYLVS KPKASQL SN MFNKKKKRTN TNSVDVLEYF SFVCGDKVPN YESMGLEIYI QASKKYKRNS FTTKVRKSST IFEVIGFALF LYSTEKKP D NFEEDGLTVE DISNPNNFSL KIVDEDGEPF EDNFGKLDRK STIQSISDSE VVLCKVDDAE KSQNEIETPL PFETGGGLM DASTLDANSS HDTTDGTINQ LSFYKPIIGN EDDIDKTNGS KIIDVTVYLY PNVNPKFNYT TISVLVTSHI NDILVKYCKM KNMDPNEYA LKVLGKNYIL DLNDTVLRLD GINKVELISK KDARELHLEK MKPDLKKPVL PTIQSNDLTP LTLEPLNSYL K ADAGGAVA AIPENTKVTS KAKKISTKYK LGLAKQHSSS SVASGSVSTA GGLANGNGFF KNKNSSKSSL HGTLQFHNIN RS QSTMEHT PDTPNGVGDN FQDLFTGAYH KYKVWRRQQM SFINKHERTL AIDGDYIYIV PPEGRIHWHD NVKTKSLHIS QVV LVKKSK RVPEHFKIFV RREGQDDIKR YYFEAVSGQE CTEIVTRLQN LLSAYRMNHK

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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: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.01 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV / Details: 2 - 3 sec blotting.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 70.0 K / Max: 70.0 K
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON II (4k x 4k) / #0 - Detector mode: INTEGRATING / #0 - Number grids imaged: 4 / #0 - Number real images: 4189 / #0 - Average exposure time: 2.3 sec. / #0 - Average electron dose: 50.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 QUANTUM (4k x 4k) / #1 - Detector mode: SUPER-RESOLUTION / #1 - Digitization - Dimensions - Width: 3710 pixel / #1 - Digitization - Dimensions - Height: 3838 pixel / #1 - Digitization - Frames/image: 1-40 / #1 - Number grids imaged: 1 / #1 - Number real images: 2847 / #1 - Average exposure time: 20.0 sec. / #1 - Average electron dose: 47.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Particle selectionNumber selected: 350000
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: EMDB MAP
EMDB ID:

2990

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 16190
Image processing ID1
Image recording ID1

-
Image processing #2

Particle selectionNumber selected: 200000
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: EMDB MAP
EMDB ID:

2990

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 10663
Image processing ID2
Image recording ID2

-
Atomic model buiding 1

Initial modelPDB ID:

5fvm


Chain - Residue range: 81-2474
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6emk:
Cryo-EM Structure of Saccharomyces cerevisiae Target of Rapamycin Complex 2

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