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Yorodumi- EMDB-50183: cryo-EM structure of LST2 TOS peptide bound to human mTOR complex 1 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50183 | |||||||||
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Title | cryo-EM structure of LST2 TOS peptide bound to human mTOR complex 1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | MTOR / MTORC1 / LST2 / ZFYVE28 / EGFR / TOS / SIGNALING PROTEIN | |||||||||
Function / homology | Function and homology information negative regulation of epidermal growth factor-activated receptor activity / RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding ...negative regulation of epidermal growth factor-activated receptor activity / RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / TORC2 complex / regulation of membrane permeability / heart valve morphogenesis / negative regulation of lysosome organization / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / TORC1 complex / calcineurin-NFAT signaling cascade / nucleus localization / cellular response to methionine / voluntary musculoskeletal movement / regulation of osteoclast differentiation / positive regulation of odontoblast differentiation / TORC1 signaling / positive regulation of keratinocyte migration / negative regulation of epidermal growth factor receptor signaling pathway / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / cellular response to nutrient / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / energy reserve metabolic process / negative regulation of cell size / ruffle organization / phosphatidylinositol-3-phosphate binding / protein serine/threonine kinase inhibitor activity / positive regulation of osteoclast differentiation / cellular response to osmotic stress / negative regulation of protein localization to nucleus / enzyme-substrate adaptor activity / anoikis / cardiac muscle cell development / positive regulation of transcription by RNA polymerase III / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / negative regulation of macroautophagy / regulation of cell size / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of oligodendrocyte differentiation / Macroautophagy / positive regulation of actin filament polymerization / lysosome organization / positive regulation of myotube differentiation / protein kinase activator activity / oligodendrocyte differentiation / behavioral response to pain / Constitutive Signaling by AKT1 E17K in Cancer / germ cell development / mTORC1-mediated signalling / CD28 dependent PI3K/Akt signaling / : / social behavior / HSF1-dependent transactivation / neuronal action potential / TOR signaling / positive regulation of TOR signaling / response to amino acid / endomembrane system / cellular response to nutrient levels / positive regulation of translational initiation / regulation of macroautophagy / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of lamellipodium assembly / positive regulation of epithelial to mesenchymal transition / positive regulation of lipid biosynthetic process / heart morphogenesis / response to nutrient / cardiac muscle contraction / regulation of cellular response to heat / phagocytic vesicle / positive regulation of stress fiber assembly / cytoskeleton organization / 14-3-3 protein binding / Regulation of PTEN gene transcription / positive regulation of endothelial cell proliferation / T cell costimulation / cellular response to starvation / phosphorylation / positive regulation of glycolytic process / cellular response to amino acid starvation / protein serine/threonine kinase activator activity / response to nutrient levels / negative regulation of autophagy / cellular response to amino acid stimulus / VEGFR2 mediated vascular permeability / post-embryonic development / positive regulation of peptidyl-threonine phosphorylation / regulation of signal transduction by p53 class mediator / regulation of autophagy Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.68 Å | |||||||||
Authors | Craigie LM / Maier T | |||||||||
Funding support | Switzerland, European Union, 2 items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: mTORC1 phosphorylates and stabilizes LST2 to negatively regulate EGFR Authors: Battaglioni S / Craigie LM / Filippini S / Maier T / Hall MN | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50183.map.gz | 257.5 MB | EMDB map data format | |
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Header (meta data) | emd-50183-v30.xml emd-50183.xml | 22.5 KB 22.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_50183_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_50183.png | 47.1 KB | ||
Filedesc metadata | emd-50183.cif.gz | 8.9 KB | ||
Others | emd_50183_half_map_1.map.gz emd_50183_half_map_2.map.gz | 474.4 MB 474.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50183 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50183 | HTTPS FTP |
-Validation report
Summary document | emd_50183_validation.pdf.gz | 700.4 KB | Display | EMDB validaton report |
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Full document | emd_50183_full_validation.pdf.gz | 699.9 KB | Display | |
Data in XML | emd_50183_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | emd_50183_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50183 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50183 | HTTPS FTP |
-Related structure data
Related structure data | 9f44MC 9f42C 9f43C 9f45C M: atomic model generated by this map C: citing same article (ref.) |
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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_50183.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_50183_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_50183_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : mTORC1 in complex with LST2 TOS peptide
Entire | Name: mTORC1 in complex with LST2 TOS peptide |
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Components |
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-Supramolecule #1: mTORC1 in complex with LST2 TOS peptide
Supramolecule | Name: mTORC1 in complex with LST2 TOS peptide / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Serine/threonine-protein kinase mTOR
Macromolecule | Name: Serine/threonine-protein kinase mTOR / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 289.257969 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MLGTGPAAAT TAATTSSNVS VLQQFASGLK SRNEETRAKA AKELQHYVTM ELREMSQEES TRFYDQLNHH IFELVSSSDA NERKGGILA IASLIGVEGG NATRIGRFAN YLRNLLPSND PVVMEMASKA IGRLAMAGDT FTAEYVEFEV KRALEWLGAD R NEGRRHAA ...String: MLGTGPAAAT TAATTSSNVS VLQQFASGLK SRNEETRAKA AKELQHYVTM ELREMSQEES TRFYDQLNHH IFELVSSSDA NERKGGILA IASLIGVEGG NATRIGRFAN YLRNLLPSND PVVMEMASKA IGRLAMAGDT FTAEYVEFEV KRALEWLGAD R NEGRRHAA VLVLRELAIS VPTFFFQQVQ PFFDNIFVAV WDPKQAIREG AVAALRACLI LTTQREPKEM QKPQWYRHTF EE AEKGFDE TLAKEKGMNR DDRIHGALLI LNELVRISSM EGERLREEME EITQQQLVHD KYCKDLMGFG TKPRHITPFT SFQ AVQPQQ SNALVGLLGY SSHQGLMGFG TSPSPAKSTL VESRCCRDLM EEKFDQVCQW VLKCRNSKNS LIQMTILNLL PRLA AFRPS AFTDTQYLQD TMNHVLSCVK KEKERTAAFQ ALGLLSVAVR SEFKVYLPRV LDIIRAALPP KDFAHKRQKA MQVDA TVFT CISMLARAMG PGIQQDIKEL LEPMLAVGLS PALTAVLYDL SRQIPQLKKD IQDGLLKMLS LVLMHKPLRH PGMPKG LAH QLASPGLTTL PEASDVGSIT LALRTLGSFE FEGHSLTQFV RHCADHFLNS EHKEIRMEAA RTCSRLLTPS IHLISGH AH VVSQTAVQVV ADVLSKLLVV GITDPDPDIR YCVLASLDER FDAHLAQAEN LQALFVALND QVFEIRELAI CTVGRLSS M NPAFVMPFLR KMLIQILTEL EHSGIGRIKE QSARMLGHLV SNAPRLIRPY MEPILKALIL KLKDPDPDPN PGVINNVLA TIGELAQVSG LEMRKWVDEL FIIIMDMLQD SSLLAKRQVA LWTLGQLVAS TGYVVEPYRK YPTLLEVLLN FLKTEQNQGT RREAIRVLG LLGALDPYKH KVNIGMIDQS RDASAVSLSE SKSSQDSSDY STSEMLVNMG NLPLDEFYPA VSMVALMRIF R DQSLSHHH TMVVQAITFI FKSLGLKCVQ FLPQVMPTFL NVIRVCDGAI REFLFQQLGM LVSFVKSHIR PYMDEIVTLM RE FWVMNTS IQSTIILLIE QIVVALGGEF KLYLPQLIPH MLRVFMHDNS PGRIVSIKLL AAIQLFGANL DDYLHLLLPP IVK LFDAPE APLPSRKAAL ETVDRLTESL DFTDYASRII HPIVRTLDQS PELRSTAMDT LSSLVFQLGK KYQIFIPMVN KVLV RHRIN HQRYDVLICR IVKGYTLADE EEDPLIYQHR MLRSGQGDAL ASGPVETGPM KKLHVSTINL QKAWGAARRV SKDDW LEWL RRLSLELLKD SSSPSLRSCW ALAQAYNPMA RDLFNAAFVS CWSELNEDQQ DELIRSIELA LTSQDIAEVT QTLLNL AEF MEHSDKGPLP LRDDNGIVLL GERAAKCRAY AKALHYKELE FQKGPTPAIL ESLISINNKL QQPEAAAGVL EYAMKHF GE LEIQATWYEK LHEWEDALVA YDKKMDTNKD DPELMLGRMR CLEALGEWGQ LHQQCCEKWT LVNDETQAKM ARMAAAAA W GLGQWDSMEE YTCMIPRDTH DGAFYRAVLA LHQDLFSLAQ QCIDKARDLL DAELTAMAGE SYSRAYGAMV SCHMLSELE EVIQYKLVPE RREIIRQIWW ERLQGCQRIV EDWQKILMVR SLVVSPHEDM RTWLKYASLC GKSGRLALAH KTLVLLLGVD PSRQLDHPL PTVHPQVTYA YMKNMWKSAR KIDAFQHMQH FVQTMQQQAQ HAIATEDQQH KQELHKLMAR CFLKLGEWQL N LQGINEST IPKVLQYYSA ATEHDRSWYK AWHAWAVMNF EAVLHYKHQN QARDEKKKLR HASGANITNA TTAATTAATA TT TASTEGS NSESEAESTE NSPTPSPLQK KVTEDLSKTL LMYTVPAVQG FFRSISLSRG NNLQDTLRVL TLWFDYGHWP DVN EALVEG VKAIQIDTWL QVIPQLIARI DTPRPLVGRL IHQLLTDIGR YHPQALIYPL TVASKSTTTA RHNAANKILK NMCE HSNTL VQQAMMVSEE LIRVAILWHE MWHEGLEEAS RLYFGERNVK GMFEVLEPLH AMMERGPQTL KETSFNQAYG RDLME AQEW CRKYMKSGNV KDLTQAWDLY YHVFRRISKQ LPQLTSLELQ YVSPKLLMCR DLELAVPGTY DPNQPIIRIQ SIAPSL QVI TSKQRPRKLT LMGSNGHEFV FLLKGHEDLR QDERVMQLFG LVNTLLANDP TSLRKNLSIQ RYAVIPLSTN SGLIGWV PH CDTLHALIRD YREKKKILLN IEHRIMLRMA PDYDHLTLMQ KVEVFEHAVN NTAGDDLAKL LWLKSPSSEV WFDRRTNY T RSLAVMSMVG YILGLGDRHP SNLMLDRLSG KILHIDFGDC FEVAMTREKF PEKIPFRLTR MLTNAMEVTG LDGNYRITC HTVMEVLREH KDSVMAVLEA FVYDPLLNWR LMDTNTKGNK RSRTRTDSYS AGQSVEILDG VELGEPAHKK TGTTVPESIH SFIGDGLVK PEALNKKAIQ IINRVRDKLT GRDFSHDDTL DVPTQVELLI KQATSHENLC QCYIGWCPFW UniProtKB: Serine/threonine-protein kinase mTOR |
-Macromolecule #2: Target of rapamycin complex subunit LST8
Macromolecule | Name: Target of rapamycin complex subunit LST8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 35.91009 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MNTSPGTVGS DPVILATAGY DHTVRFWQAH SGICTRTVQH QDSQVNALEV TPDRSMIAAA GYQHIRMYDL NSNNPNPIIS YDGVNKNIA SVGFHEDGRW MYTGGEDCTA RIWDLRSRNL QCQRIFQVNA PINCVCLHPN QAELIVGDQS GAIHIWDLKT D HNEQLIPE ...String: MNTSPGTVGS DPVILATAGY DHTVRFWQAH SGICTRTVQH QDSQVNALEV TPDRSMIAAA GYQHIRMYDL NSNNPNPIIS YDGVNKNIA SVGFHEDGRW MYTGGEDCTA RIWDLRSRNL QCQRIFQVNA PINCVCLHPN QAELIVGDQS GAIHIWDLKT D HNEQLIPE PEVSITSAHI DPDASYMAAV NSTGNCYVWN LTGGIGDEVT QLIPKTKIPA HTRYALQCRF SPDSTLLATC SA DQTCKIW RTSNFSLMTE LSIKSGNPGE SSRGWMWGCA FSGDSQYIVT ASSDNLARLW CVETGEIKRE YGGHQKAVVC LAF NDSVLG UniProtKB: Target of rapamycin complex subunit LST8 |
-Macromolecule #3: Regulatory-associated protein of mTOR
Macromolecule | Name: Regulatory-associated protein of mTOR / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 152.764656 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: HHHHHHHHHH EQKLISEEDL DYKDDDDKME SEMLQSPLLG LGEEDEADLT DWNLPLAFMK KRHCEKIEGS KSLAQSWRMK DRMKTVSVA LVLCLNVGVD PPDVVKTTPC ARLECWIDPL SMGPQKALET IGANLQKQYE NWQPRARYKQ SLDPTVDEVK K LCTSLRRN ...String: HHHHHHHHHH EQKLISEEDL DYKDDDDKME SEMLQSPLLG LGEEDEADLT DWNLPLAFMK KRHCEKIEGS KSLAQSWRMK DRMKTVSVA LVLCLNVGVD PPDVVKTTPC ARLECWIDPL SMGPQKALET IGANLQKQYE NWQPRARYKQ SLDPTVDEVK K LCTSLRRN AKEERVLFHY NGHGVPRPTV NGEVWVFNKN YTQYIPLSIY DLQTWMGSPS IFVYDCSNAG LIVKSFKQFA LQ REQELEV AAINPNHPLA QMPLPPSMKN CIQLAACEAT ELLPMIPDLP ADLFTSCLTT PIKIALRWFC MQKCVSLVPG VTL DLIEKI PGRLNDRRTP LGELNWIFTA ITDTIAWNVL PRDLFQKLFR QDLLVASLFR NFLLAERIMR SYNCTPVSSP RLPP TYMHA MWQAWDLAVD ICLSQLPTII EEGTAFRHSP FFAEQLTAFQ VWLTMGVENR NPPEQLPIVL QVLLSQVHRL RALDL LGRF LDLGPWAVSL ALSVGIFPYV LKLLQSSARE LRPLLVFIWA KILAVDSSCQ ADLVKDNGHK YFLSVLADPY MPAEHR TMT AFILAVIVNS YHTGQEACLQ GNLIAICLEQ LNDPHPLLRQ WVAICLGRIW QNFDSARWCG VRDSAHEKLY SLLSDPI PE VRCAAVFALG TFVGNSAERT DHSTTIDHNV AMMLAQLVSD GSPMVRKELV VALSHLVVQY ESNFCTVALQ FIEEEKNY A LPSPATTEGG SLTPVRDSPC TPRLRSVSSY GNIRAVATAR SLNKSLQNLS LTEESGGAVA FSPGNLSTSS SASSTLGSP ENEEHILSFE TIDKMRRASS YSSLNSLIGV SFNSVYTQIW RVLLHLAADP YPEVSDVAMK VLNSIAYKAT VNARPQRVLD TSSLTQSAP ASPTNKGVHI HQAGGSPPAS STSSSSLTND VAKQPVSRDL PSGRPGTTGP AGAQYTPHSH QFPRTRKMFD K GPEQTADD ADDAAGHKSF ISATVQTGFC DWSARYFAQP VMKIPEEHDL ESQIRKEREW RFLRNSRVRR QAQQVIQKGI TR LDDQIFL NRNPGVPSVV KFHPFTPCIA VADKDSICFW DWEKGEKLDY FHNGNPRYTR VTAMEYLNGQ DCSLLLTATD DGA IRVWKN FADLEKNPEM VTAWQGLSDM LPTTRGAGMV VDWEQETGLL MSSGDVRIVR IWDTDREMKV QDIPTGADSC VTSL SCDSH RSLIVAGLGD GSIRVYDRRM ALSECRVMTY REHTAWVVKA SLQKRPDGHI VSVSVNGDVR IFDPRMPESV NVLQI VKGL TALDIHPQAD LIACGSVNQF TAIYNSSGEL INNIKYYDGF MGQRVGAISC LAFHPHWPHL AVGSNDYYIS VYSVEK RVR UniProtKB: Regulatory-associated protein of mTOR |
-Macromolecule #4: Lateral signaling target protein 2 homolog
Macromolecule | Name: Lateral signaling target protein 2 homolog / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 1.660733 KDa |
Sequence | String: DEEERVFFMD DVE UniProtKB: Lateral signaling target protein 2 homolog |
-Macromolecule #5: INOSITOL HEXAKISPHOSPHATE
Macromolecule | Name: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: IHP |
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Molecular weight | Theoretical: 660.035 Da |
Chemical component information | ChemComp-IHP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4470 / Average electron dose: 48.43 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |