+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13097 | ||||||||||||
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Title | human DEPTOR in a complex with mutant human mTORC1 A1459P | ||||||||||||
Map data | mTORC1 with mTOR A1459P mutant in a complex with DEPTOR | ||||||||||||
Sample |
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Keywords | kinase / PIKK / mTOR / cancer-associated mutation / DEPTOR / partial inhibitor / cancer / PDZ / non-canonical PDZ binding / SIGNALING PROTEIN | ||||||||||||
Function / homology | Function and homology information negative regulation of TORC2 signaling / regulation of extrinsic apoptotic signaling pathway / positive regulation of cytoplasmic translational initiation / positive regulation of pentose-phosphate shunt / RNA polymerase III type 1 promoter sequence-specific DNA binding / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation ...negative regulation of TORC2 signaling / regulation of extrinsic apoptotic signaling pathway / positive regulation of cytoplasmic translational initiation / positive regulation of pentose-phosphate shunt / RNA polymerase III type 1 promoter sequence-specific DNA binding / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / regulation of membrane permeability / TFIIIC-class transcription factor complex binding / heart valve morphogenesis / negative regulation of lysosome organization / RNA polymerase III type 3 promoter sequence-specific DNA binding / TORC2 complex / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / regulation of autophagosome assembly / calcineurin-NFAT signaling cascade / nucleus localization / TORC1 signaling / voluntary musculoskeletal movement / positive regulation of odontoblast differentiation / regulation of osteoclast differentiation / positive regulation of keratinocyte migration / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / cellular response to nutrient / energy reserve metabolic process / phosphatidic acid binding / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of cell size / ruffle organization / protein serine/threonine kinase inhibitor activity / positive regulation of osteoclast differentiation / cellular response to osmotic stress / enzyme-substrate adaptor activity / negative regulation of protein localization to nucleus / anoikis / cardiac muscle cell development / negative regulation of TOR signaling / positive regulation of transcription by RNA polymerase III / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / regulation of cell size / Macroautophagy / positive regulation of oligodendrocyte differentiation / negative regulation of macroautophagy / positive regulation of actin filament polymerization / lysosome organization / positive regulation of myotube differentiation / protein kinase inhibitor activity / protein kinase activator activity / behavioral response to pain / oligodendrocyte differentiation / Constitutive Signaling by AKT1 E17K in Cancer / mTORC1-mediated signalling / germ cell development / CD28 dependent PI3K/Akt signaling / cellular response to nutrient levels / positive regulation of phosphoprotein phosphatase activity / social behavior / HSF1-dependent transactivation / positive regulation of TOR signaling / TOR signaling / neuronal action potential / positive regulation of translational initiation / response to amino acid / positive regulation of G1/S transition of mitotic cell cycle / regulation of macroautophagy / endomembrane system / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of autophagy / positive regulation of lamellipodium assembly / positive regulation of epithelial to mesenchymal transition / positive regulation of lipid biosynthetic process / heart morphogenesis / cardiac muscle contraction / regulation of cellular response to heat / positive regulation of stress fiber assembly / negative regulation of TORC1 signaling / 14-3-3 protein binding / positive regulation of endothelial cell proliferation / cytoskeleton organization / T cell costimulation / cellular response to amino acid starvation / phagocytic vesicle / positive regulation of glycolytic process / cellular response to starvation / negative regulation of autophagy / protein serine/threonine kinase activator activity / response to nutrient levels / response to nutrient / post-embryonic development / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / regulation of signal transduction by p53 class mediator / Regulation of PTEN gene transcription Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||||||||
Authors | Heimhalt M / Berndt A | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Elife / Year: 2021 Title: Bipartite binding and partial inhibition links DEPTOR and mTOR in a mutually antagonistic embrace. Authors: Maren Heimhalt / Alex Berndt / Jane Wagstaff / Madhanagopal Anandapadamanaban / Olga Perisic / Sarah Maslen / Stephen McLaughlin / Conny Wing-Heng Yu / Glenn R Masson / Andreas Boland / ...Authors: Maren Heimhalt / Alex Berndt / Jane Wagstaff / Madhanagopal Anandapadamanaban / Olga Perisic / Sarah Maslen / Stephen McLaughlin / Conny Wing-Heng Yu / Glenn R Masson / Andreas Boland / Xiaodan Ni / Keitaro Yamashita / Garib N Murshudov / Mark Skehel / Stefan M Freund / Roger L Williams / Abstract: The mTORC1 kinase complex regulates cell growth, proliferation, and survival. Because mis-regulation of DEPTOR, an endogenous mTORC1 inhibitor, is associated with some cancers, we reconstituted ...The mTORC1 kinase complex regulates cell growth, proliferation, and survival. Because mis-regulation of DEPTOR, an endogenous mTORC1 inhibitor, is associated with some cancers, we reconstituted mTORC1 with DEPTOR to understand its function. We find that DEPTOR is a unique mTORC1 inhibitor that may have evolved to preserve feedback inhibition of PI3K. Counterintuitively, mTORC1 activated by RHEB or oncogenic mutation is much more potently inhibited by DEPTOR. Although DEPTOR partially inhibits mTORC1, mTORC1 prevents this inhibition by phosphorylating DEPTOR, a mutual antagonism that requires no exogenous factors. Structural analyses of the mTORC1/DEPTOR complex showed DEPTOR's PDZ domain interacting with the mTOR FAT region, and the unstructured linker preceding the PDZ binding to the mTOR FRB domain. The linker and PDZ form the minimal inhibitory unit, but the N-terminal tandem DEP domains also significantly contribute to inhibition. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13097.map.gz | 74.5 MB | EMDB map data format | |
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Header (meta data) | emd-13097-v30.xml emd-13097.xml | 28.2 KB 28.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13097_fsc.xml | 14.3 KB | Display | FSC data file |
Images | emd_13097.png | 78.8 KB | ||
Masks | emd_13097_msk_1.map | 80.2 MB | Mask map | |
Filedesc metadata | emd-13097.cif.gz | 9.9 KB | ||
Others | emd_13097_half_map_1.map.gz emd_13097_half_map_2.map.gz | 72.6 MB 72.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13097 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13097 | HTTPS FTP |
-Validation report
Summary document | emd_13097_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_13097_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_13097_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | emd_13097_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13097 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13097 | HTTPS FTP |
-Related structure data
Related structure data | 7owgMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13097.map.gz / Format: CCP4 / Size: 80.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | mTORC1 with mTOR A1459P mutant in a complex with DEPTOR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_13097_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: mTORC1 with mTOR A1459P mutant in a complex with DEPTOR half map 2
File | emd_13097_half_map_1.map | ||||||||||||
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Annotation | mTORC1 with mTOR A1459P mutant in a complex with DEPTOR half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: mTORC1 with mTOR A1459P mutant in a complex with DEPTOR half map 1
File | emd_13097_half_map_2.map | ||||||||||||
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Annotation | mTORC1 with mTOR A1459P mutant in a complex with DEPTOR half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : COMPLEX OF HUMAN MUTANT MTORC1 A1459P WITH THE INHIBITORY PROTEIN...
Entire | Name: COMPLEX OF HUMAN MUTANT MTORC1 A1459P WITH THE INHIBITORY PROTEIN DEPTOR |
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Components |
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-Supramolecule #1: COMPLEX OF HUMAN MUTANT MTORC1 A1459P WITH THE INHIBITORY PROTEIN...
Supramolecule | Name: COMPLEX OF HUMAN MUTANT MTORC1 A1459P WITH THE INHIBITORY PROTEIN DEPTOR type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: An mTORC1 complex bound to two copies of DEPTOR. Each mTORC1 complex consists of a dimer of an mTOR/LST8/RAPTOR heterotrimer. The mTOR is an A1459P mutant. |
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Molecular weight | Theoretical: 46.3 MDa |
-Supramolecule #2: mTORC1 with mutant A1459P mTOR
Supramolecule | Name: mTORC1 with mutant A1459P mTOR / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #4 / Details: mTORC1 with mutant A1459P mTOR |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: DEPTOR
Supramolecule | Name: DEPTOR / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 / Details: DEPTOR is a natural inhibitor of mTORC1 |
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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: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 287.570312 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MLGTGPAAAT TAATTS(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)SRNEET(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)EMSQE ...String: MLGTGPAAAT TAATTS(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)SRNEET(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)EMSQE E(UNK)TRFYDQLN HHIFELVSSS DANERKGGIL AIASLIGVEG GNATRI GRF ANYLRNLLPS NDPVVMEMAS KAIGRLAMAG DTFTAEYVEF EVKRALEWLG ADRNEGRRHA AVLVLRELAI SVPTFFF QQ VQPFFDNIFV AVWDPKQAIR EGAVAALRAC LILTTQREPK EMQKPQWYRH TFEEAEKGFD ETLAKEKGMN RDDRIHGA L LILNELVRIS SMEGERLREE MEEITQQQLV HDKYCKDLMG FGTKPRHITP FTSFQAVQPQ QSNALVGLLG YSSHQGLMG FGTSPSPAKS T(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)KCRNS KNSLIQMTIL NLLPRLAAFR PSAFT DTQY LQDTMNHVLS CVKKEKERTA AFQALGLLSV AVRSEFKVYL PRVLDIIRAA LPPKDFAHKR QKAMQVDATV FTCISM LAR AMGPGIQQDI KELLEPMLAV GLSPALTAVL YDLSRQIPQL KKDIQDGLLK MLSLVLMHKP LRHPGMPKGL AHQLASP GL TTLPEASDVG SITLALRTLG SFEFEGHSLT QFVRHCADHF LNSEHKEIRM EAARTCSRLL TPSIHLISGH AHVVSQTA V QVVADVLSKL LVVGITDPDP DIRYCVLASL DERFDAHLAQ AENLQALFVA LNDQVFEIRE LAICTVGRLS SMNPAFVMP FLRKMLIQIL TELEHSGIGR IKEQSARMLG HLVSNAPRLI RPYMEPILKA LILKLKDPDP DPNPGVINNV LATIGELAQV SGLEMRKWV DELFIIIMDM LQDSSLLAKR QVALWTLGQL VASTGYVVEP YRKYPTLLEV LLNFLKTEQN QGTRREAIRV L GLLGALDP YKHKVNIGMI DQSRDASAVS LSESKSSQDS SDYSTSEMLV NMGNLPLDEF YPAVSMVALM RIFRDQSLSH HH TMVVQAI TFIFKSLGLK CVQFLPQVMP TFLNVIRVCD GAIREFLFQQ LGMLVSFVKS HIRPYMDEIV TLMREFWVMN TSI QSTIIL LIEQIVVALG GEFKLYLPQL IPHMLRVFMH DNSPGRIVSI KLLAAIQLFG ANLDDYLHLL LPPIVKLFDA PEAP LPSRK AALETVDRLT ESLDFTDYAS RIIHPIVRTL DQSPELRSTA MDTLSSLVFQ LGKKYQIFIP MVNKVLVRHR INHQR YDVL ICRIVKGYTL ADEEEDPLIY QHRMLRSGQG DALASGPVET GPMKKLHVST INLQKAWGAA RRVSKDDWLE WLRRLS LEL LKDSSSPSLR SCWALAQAYN PMARDLFNAA FVSCWSELNE DQQDELIRSI ELALTSQDIA EVTQTLLNLA EFMEHSD KG PLPLRDDNGI VLLGERAAKC RAYAKALHYK ELEFQKGPTP AILESLISIN NKLQQPEAAA GVLEYAMKHF GELEIQAT W YEKLHEWEDP LVAYDKKMDT NKDDPELMLG RMRCLEALGE WGQLHQQCCE KWTLVNDETQ AKMARMAAAA AWGLGQWDS MEEYTCMIPR DTHDGAFYRA VLALHQDLFS LAQQCIDKAR DLLDAELTAM AGESYSRAYG AMVSCHMLSE LEEVIQYKLV PERREIIRQ IWWERLQGCQ RIVEDWQKIL MVRSLVVSPH EDMRTWLKYA SLCGKSGRLA LAHKTLVLLL GVDPSRQLDH P LPTVHPQV TYAYMKNMWK SARKIDAFQH MQHFVQTMQQ QAQHAIATED QQHKQELHKL MARCFLKLGE WQLNLQGINE ST IPKVLQY YSAATEHDRS WYKAWHAWAV MNFEAVLHYK HQNQARDEKK KLRHASGANI TNATTAATTA ATATTTASTE GSN SESEAE STENSPTPSP LQKKVTEDLS KTLLMYTVPA VQGFFRSISL SRGNNLQDTL RVLTLWFDYG HWPDVNEALV EGVK AIQID TWLQVIPQLI ARIDTPRPLV GRLIHQLLTD IGRYHPQALI YPLTVASKST TTARHNAANK ILKNMCEHSN TLVQQ AMMV SEELIRVAIL WHEMWHEGLE EASRLYFGER NVKGMFEVLE PLHAMMERGP QTLKETSFNQ AYGRDLMEAQ EWCRKY MKS GNVKDLTQAW DLYYHVFRRI SKQLPQLTSL ELQYVSPKLL MCRDLELAVP GTYDPNQPII RIQSIAPSLQ VITSKQR PR KLTLMGSNGH EFVFLLKGHE DLRQDERVMQ LFGLVNTLLA NDPTSLRKNL SIQRYAVIPL STNSGLIGWV PHCDTLHA L IRDYREKKKI LLNIEHRIML RMAPDYDHLT LMQKVEVFEH AVNNTAGDDL AKLLWLKSPS SEVWFDRRTN YTRSLAVMS MVGYILGLGD RHPSNLMLDR LSGKILHIDF GDCFEVAMTR EKFPEKIPFR LTRMLTNAME VTGLDGNYRI TCHTVMEVLR EHKDSVMAV LEAFVYDPLL NWRLMDTNTK GNKRSRTRTD SYSAGQSVEI LDGVELGEPA HKKTGTTVPE SIHSFIGDGL V KPEALNKK AIQIINRVRD KLTGRDFSHD DTLDVPTQVE LLIKQATSHE NLCQCYIGWC PFW UniProtKB: Serine/threonine-protein kinase mTOR, Serine/threonine-protein kinase mTOR, Serine/threonine-protein kinase mTOR, 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: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 35.91009 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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: DEP domain-containing mTOR-interacting protein
Macromolecule | Name: DEP domain-containing mTOR-interacting protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 46.365832 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MEEGGSTGSA GSDSSTSGSG GAQQRELERM AEVLVTGEQL RLRLHEEKVI KDRRHHLKTY PNCFVAKELI DWLIEHKEAS DRETAIKLM QKLADRGIIH HVCDEHKEFK DVKLFYRFRK DDGTFPLDNE VKAFMRGQRL YEKLMSPENT LLQPREEEGV K YERTFMAS ...String: MEEGGSTGSA GSDSSTSGSG GAQQRELERM AEVLVTGEQL RLRLHEEKVI KDRRHHLKTY PNCFVAKELI DWLIEHKEAS DRETAIKLM QKLADRGIIH HVCDEHKEFK DVKLFYRFRK DDGTFPLDNE VKAFMRGQRL YEKLMSPENT LLQPREEEGV K YERTFMAS EFLDWLVQEG EATTRKEAEQ LCHRLMEHGI IQHVSSKHPF VDSNLLYQFR MNFRRRRRLM ELLNEKSPSS QE THDSPFC LRKQSHDNRK STSFMSVSPS KEIKIVSAVR RSSMSSCGSS GYFSSSPTLS SSPPVLCNPK SVLKRPVTSE ELL TPGAPY ARKTFTIVGD AVGWGFVVRG SKPCHIQAVD PSGPAAAAGM KVCQFVVSVN GLNVLHVDYR TVNNLILTGP RTIV MEVME ELEC UniProtKB: DEP domain-containing mTOR-interacting protein |
-Macromolecule #4: Regulatory-associated protein of mTOR
Macromolecule | Name: Regulatory-associated protein of mTOR / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 149.200016 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MESEMLQSPL LGLGEEDEAD LTDWNLPLAF MKKRHCEKIE GSKSLAQSWR MKDRMKTVSV ALVLCLNVGV DPPDVVKTTP CARLECWID PLSMGPQKAL ETIGANLQKQ YENWQPRARY KQSLDPTVDE VKKLCTSLRR NAKEERVLFH YNGHGVPRPT V NGEVWVFN ...String: MESEMLQSPL LGLGEEDEAD LTDWNLPLAF MKKRHCEKIE GSKSLAQSWR MKDRMKTVSV ALVLCLNVGV DPPDVVKTTP CARLECWID PLSMGPQKAL ETIGANLQKQ YENWQPRARY KQSLDPTVDE VKKLCTSLRR NAKEERVLFH YNGHGVPRPT V NGEVWVFN KNYTQYIPLS IYDLQTWMGS PSIFVYDCSN AGLIVKSFKQ FALQREQELE VAAINPNHPL AQMPLPPSMK NC IQLAACE ATELLPMIPD LPADLFTSCL TTPIKIALRW FCMQKCVSLV PGVTLDLIEK IPGRLNDRRT PLGELNWIFT AIT DTIAWN VLPRDLFQKL FRQDLLVASL FRNFLLAERI MRSYNCTPVS SPRLPPTYMH AMWQAWDLAV DICLSQLPTI IEEG TAFRH SPFFAEQLTA FQVWLTMGVE NRNPPEQLPI VLQVLLSQVH RLRALDLLGR FLDLGPWAVS LALSVGIFPY VLKLL QSSA RELRPLLVFI WAKILAVDSS CQADLVKDNG HKYFLSVLAD PYMPAEHRTM TAFILAVIVN SYHTGQEACL QGNLIA ICL EQLNDPHPLL RQWVAICLGR IWQNFDSARW CGVRDSAHEK LYSLLSDPIP EVRCAAVFAL GTFVGNSAER TDHSTTI DH NVAMMLAQLV SDGSPMVRKE LVVALSHLVV QYESNFCTVA LQFIEEEKNY ALPSPATTEG GSLTPVRDSP CTPRLRSV S SYGNIRAVAT ARSLNKSLQN LSLTEESGGA VAFSPGNLST SSSASSTLGS PENEEHILSF ETIDKMRRAS SYSSLNSLI GVSFNSVYTQ IWRVLLHLAA DPYPEVSDVA MKVLNSIAYK ATVNARPQRV LDTSSLTQSA PASPTNKGVH IHQAGGSPPA SSTSSSSLT NDVAKQPVSR DLPSGRPGTT GPAGAQYTPH SHQFPRTRKM FDKGPEQTAD DADDAAGHKS FISATVQTGF C DWSARYFA QPVMKIPEEH DLESQIRKER EWRFLRNSRV RRQAQQVIQK GITRLDDQIF LNRNPGVPSV VKFHPFTPCI AV ADKDSIC FWDWEKGEKL DYFHNGNPRY TRVTAMEYLN GQDCSLLLTA TDDGAIRVWK NFADLEKNPE MVTAWQGLSD MLP TTRGAG MVVDWEQETG LLMSSGDVRI VRIWDTDREM KVQDIPTGAD SCVTSLSCDS HRSLIVAGLG DGSIRVYDRR MALS ECRVM TYREHTAWVV KASLQKRPDG HIVSVSVNGD VRIFDPRMPE SVNVLQIVKG LTALDIHPQA DLIACGSVNQ FTAIY NSSG ELINNIKYYD GFMGQRVGAI SCLAFHPHWP HLAVGSNDYY ISVYSVEKRV R UniProtKB: Regulatory-associated protein of mTOR |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.6 mg/mL |
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Buffer | pH: 7.5 Details: 50 mM HEPES, pH 7.5, 200 mM NaCl, 1 mM TCEP, 1 mM MgCl2, 500 uM AMP-PNP |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 287 K / Instrument: FEI VITROBOT MARK I / Details: blotting time of 2 s and a force of -15.. |
Details | Purified mutant mTORC1 A1459P and DEPTOR were preincubated in the presence of MgCl2 and AMP-PNP for 20 min and used for cryo-EM grid preparation. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 100.0 K / Max: 100.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 6000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 2 / Number real images: 4759 / Average exposure time: 2.5 sec. / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -3.0 µm / Nominal defocus min: -1.4000000000000001 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: B / Chain - Residue range: 1-2549 / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT / Overall B value: 145.7 / Target criteria: Correlation |
Output model | PDB-7owg: |