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- EMDB-7087: mTORC1 structure refined to 3.0 angstroms -

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Basic information

Entry
Database: EMDB / ID: EMD-7087
TitlemTORC1 structure refined to 3.0 angstroms
Map dataPrimary consensus dimer map in C2.
Sample
  • Complex: Dimer of two mTOR-mLST8-RAPTOR-4EBP1 complexes.
    • Protein or peptide: Serine/threonine-protein kinase mTOR
    • Protein or peptide: Target of rapamycin complex subunit LST8MTOR
    • Protein or peptide: Regulatory-associated protein of mTOR
    • Protein or peptide: Eukaryotic translation initiation factor 4E-binding protein 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsPIKK / TRANSFERASE
Function / homology
Function and homology information


RNA polymerase III type 2 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of pentose-phosphate shunt / T-helper 1 cell lineage commitment / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / eukaryotic initiation factor 4E binding / cellular response to leucine starvation ...RNA polymerase III type 2 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of pentose-phosphate shunt / T-helper 1 cell lineage commitment / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / eukaryotic initiation factor 4E binding / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / TORC2 complex / heart valve morphogenesis / regulation of membrane permeability / negative regulation of lysosome organization / RNA polymerase III type 3 promoter sequence-specific DNA binding / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / regulation of autophagosome assembly / TORC1 signaling / positive regulation of odontoblast differentiation / voluntary musculoskeletal movement / 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 / Energy dependent regulation of mTOR by LKB1-AMPK / nucleus localization / ruffle organization / protein serine/threonine kinase inhibitor activity / negative regulation of cell size / cellular response to osmotic stress / positive regulation of osteoclast differentiation / enzyme-substrate adaptor activity / anoikis / cardiac muscle cell development / positive regulation of transcription by RNA polymerase III / negative regulation of protein localization to nucleus / regulation of myelination / negative regulation of calcineurin-NFAT signaling cascade / Macroautophagy / regulation of cell size / negative regulation of macroautophagy / lysosome organization / positive regulation of oligodendrocyte differentiation / positive regulation of actin filament polymerization / protein kinase activator activity / positive regulation of myotube differentiation / behavioral response to pain / TOR signaling / oligodendrocyte differentiation / mTORC1-mediated signalling / germ cell development / Constitutive Signaling by AKT1 E17K in Cancer / social behavior / cellular response to nutrient levels / CD28 dependent PI3K/Akt signaling / positive regulation of phosphoprotein phosphatase activity / positive regulation of translational initiation / neuronal action potential / HSF1-dependent transactivation / positive regulation of TOR signaling / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of epithelial to mesenchymal transition / regulation of macroautophagy / endomembrane system / 'de novo' pyrimidine nucleobase biosynthetic process / response to amino acid / positive regulation of lipid biosynthetic process / phagocytic vesicle / positive regulation of lamellipodium assembly / translation initiation factor binding / heart morphogenesis / regulation of cellular response to heat / cytoskeleton organization / negative regulation of translational initiation / translation repressor activity / cardiac muscle contraction / positive regulation of stress fiber assembly / cellular response to amino acid starvation / T cell costimulation / cellular response to starvation / positive regulation of endothelial cell proliferation / positive regulation of glycolytic process / protein serine/threonine kinase activator activity / positive regulation of mitotic cell cycle / response to nutrient levels / post-embryonic development / negative regulation of autophagy / response to nutrient / 14-3-3 protein binding / VEGFR2 mediated vascular permeability / positive regulation of translation / positive regulation of peptidyl-threonine phosphorylation / regulation of signal transduction by p53 class mediator / Regulation of PTEN gene transcription
Similarity search - Function
Eukaryotic translation initiation factor 4E binding / Eukaryotic translation initiation factor 4E binding protein (EIF4EBP) / 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 ...Eukaryotic translation initiation factor 4E binding / Eukaryotic translation initiation factor 4E binding protein (EIF4EBP) / 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 / Rapamycin binding domain / PIK-related kinase, FAT / FAT domain / FATC domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Quinoprotein alcohol dehydrogenase-like superfamily / 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 mTOR / Eukaryotic translation initiation factor 4E-binding protein 1 / Regulatory-associated protein of mTOR / Target of rapamycin complex subunit LST8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsPavletich NP / Yang H
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2017
Title: Mechanisms of mTORC1 activation by RHEB and inhibition by PRAS40.
Authors: Haijuan Yang / Xiaolu Jiang / Buren Li / Hyo J Yang / Meredith Miller / Angela Yang / Ankita Dhar / Nikola P Pavletich /
Abstract: The mechanistic target of rapamycin complex 1 (mTORC1) controls cell growth and metabolism in response to nutrients, energy levels, and growth factors. It contains the atypical kinase mTOR and the ...The mechanistic target of rapamycin complex 1 (mTORC1) controls cell growth and metabolism in response to nutrients, energy levels, and growth factors. It contains the atypical kinase mTOR and the RAPTOR subunit that binds to the Tor signalling sequence (TOS) motif of substrates and regulators. mTORC1 is activated by the small GTPase RHEB (Ras homologue enriched in brain) and inhibited by PRAS40. Here we present the 3.0 ångström cryo-electron microscopy structure of mTORC1 and the 3.4 ångström structure of activated RHEB-mTORC1. RHEB binds to mTOR distally from the kinase active site, yet causes a global conformational change that allosterically realigns active-site residues, accelerating catalysis. Cancer-associated hyperactivating mutations map to structural elements that maintain the inactive state, and we provide biochemical evidence that they mimic RHEB relieving auto-inhibition. We also present crystal structures of RAPTOR-TOS motif complexes that define the determinants of TOS recognition, of an mTOR FKBP12-rapamycin-binding (FRB) domain-substrate complex that establishes a second substrate-recruitment mechanism, and of a truncated mTOR-PRAS40 complex that reveals PRAS40 inhibits both substrate-recruitment sites. These findings help explain how mTORC1 selects its substrates, how its kinase activity is controlled, and how it is activated by cancer-associated mutations.
History
DepositionOct 20, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseDec 20, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6bcx
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7087.png

Downloads & links

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Map

FileDownload / File: emd_7087.map.gz / Format: CCP4 / Size: 199.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary consensus dimer map in C2.
Voxel sizeX=Y=Z: 1.3306 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.17757502 - 0.28161508
Average (Standard dev.)0.0000037334783 (±0.0050782706)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions374374374
Spacing374374374
CellA=B=C: 497.6444 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.33059893048131.33059893048131.3305989304813
M x/y/z374374374
origin x/y/z0.0000.0000.000
length x/y/z497.644497.644497.644
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS374374374
D min/max/mean-0.1780.2820.000

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Supplemental data

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Additional map: Focused 3D refinement of monomer part1 (mask 1)...

Fileemd_7087_additional_1.map
AnnotationFocused 3D refinement of monomer part1 (mask 1) used to reconstruct the 3.0 angstroms resolution C2 dimer structure factors with the REFMAC5 composite map option for model refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused 3D refinement of monomer part2 (mask 2)...

Fileemd_7087_additional_2.map
AnnotationFocused 3D refinement of monomer part2 (mask 2) used to reconstruct the 3.0 angstroms resolution C2 dimer structure factors with the REFMAC5 composite map option for model refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused 3D refinement of monomer part3 (mask 3)...

Fileemd_7087_additional_3.map
AnnotationFocused 3D refinement of monomer part3 (mask 3) used to reconstruct the 3.0 angstroms resolution C2 dimer structure factors with the REFMAC5 composite map option for model refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimer of two mTOR-mLST8-RAPTOR-4EBP1 complexes.

EntireName: Dimer of two mTOR-mLST8-RAPTOR-4EBP1 complexes.
Components
  • Complex: Dimer of two mTOR-mLST8-RAPTOR-4EBP1 complexes.
    • Protein or peptide: Serine/threonine-protein kinase mTOR
    • Protein or peptide: Target of rapamycin complex subunit LST8MTOR
    • Protein or peptide: Regulatory-associated protein of mTOR
    • Protein or peptide: Eukaryotic translation initiation factor 4E-binding protein 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Dimer of two mTOR-mLST8-RAPTOR-4EBP1 complexes.

SupramoleculeName: Dimer of two mTOR-mLST8-RAPTOR-4EBP1 complexes. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serine/threonine-protein kinase mTOR

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 287.399125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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)(UNK)(UNK)RNS KNSLIQMTIL NLLPRLA AF RPSAFTDTQY LQDTMNHVLS CVKKEKERTA AFQALGLLSV AVRSEFKVYL PRVLDIIRAA LPPKDFAHKR QKAMQVDA T VFTCISMLAR AMGPGIQQDI KELLEPMLAV GLSPALTAVL YDLSRQIPQL KKDIQDGLLK MLSLVLM(UNK)KP LRHPG MPKG LAHQLASPGL TTLPEAS(UNK)VG SITLALRTLG SFEFEGHSLT QFVRHCADHF LNSEHKEIRM EAARTCSRLL TP SIHLISG HAHVVSQTAV QVVADVLSKL LVVGITDPDP DIRYCVLASL DERFDAHLAQ AENLQALFVA LNDQVFEIRE LAI CTVGRL SSMNPAFVMP FLRKMLIQIL TELEHSGIGR IKEQSARMLG HLVSNAPRLI RPYMEPILKA LILKLKDPDP DPNP GVINN VLATIGELAQ VSGLEMRKWV DELFIIIMDM LQDSSLLAKR QVALWTLGQL VASTGYVVEP YRKYPTLLEV LLNFL KTEQ NQGTRREAIR VLGLLGALDP YKHKVNIGMI DQSRDASAVS LSESKSSQDS SDYSTSEMLV NMGNLPLDEF YPAVSM VAL MRIFRDQSLS HHHTMVVQAI TFIFKSLGLK CVQFLPQVMP TFLNVIRVCD GAIREFLFQQ LGMLVSFVKS HIRPYMD EI VTLMREFWVM NTSIQSTIIL LIEQIVVALG GEFKLYLPQL IPHMLRVFMH DNSPGRIVSI KLLAAIQLFG ANLDDYLH L LLPPIVKLFD APEAPLPSRK AALETVDRLT ESLDFTDYAS RIIHPIVRTL DQSPELRSTA MDTLSSLVFQ LGKKYQIFI PMVNKVLVRH RINHQRYDVL ICRIVKGYTL ADEEEDPLIY QHRMLRSGQG DALASGPVET GPMKKLHVST INLQKAWGAA RRVSKDDWL EWLRRLSLEL LKDSSSPSLR SCWALAQAYN PMARDLFNAA FVSCWSELNE DQQDELIRSI ELALTSQDIA E VTQTLLNL AEFMEHSDKG PLPLRDDNGI VLLGERAAKC RAYAKALHYK ELEFQKGPTP AILESLISIN NKLQQPEAAA GV LEYAMKH FGELEIQATW YEKLHEWEDA LVAYDKKMDT NKDDPELMLG RMRCLEALGE WGQLHQQCCE KWTLVNDETQ AKM ARMAAA AAWGLGQWDS MEEYTCMIPR DTHDGAFYRA VLALHQDLFS LAQQCIDKAR DLLDAELTAM AGESYSRAYG AMVS CHMLS ELEEVIQYKL VPERREIIRQ IWWERLQGCQ RIVEDWQKIL MVRSLVVSPH EDMRTWLKYA SLCGKSGRLA LAHKT LVLL LGVDPSRQLD HPLPTVHPQV TYAYMKNMWK SARKIDAFQH MQHFVQTMQQ QAQHAIATED QQHKQELHKL MARCFL KLG EWQLNLQGIN ESTIPKVLQY YSAATEHDRS WYKAWHAWAV MNFEAVLHYK HQNQARDEKK KLRHASGANI TNATTAA TT AATATTTAST EGSNSESEAE STENSPTPSP LQKKVTEDLS KTLLMYTVPA VQGFFRSISL SRGNNLQDTL RVLTLWFD Y GHWPDVNEAL VEGVKAIQID TWLQVIPQLI ARIDTPRPLV GRLIHQLLTD IGRYHPQALI YPLTVASKST TTARHNAAN KILKNMCEHS NTLVQQAMMV SEELIRVAIL WHEMWHEGLE EASRLYFGER NVKGMFEVLE PLHAMMERGP QTLKETSFNQ AYGRDLMEA QEWCRKYMKS GNVKDLTQAW DLYYHVFRRI SKQLPQLTSL ELQYVSPKLL MCRDLELAVP GTYDPNQPII R IQSIAPSL QVITSKQRPR KLTLMGSNGH EFVFLLKGHE DLRQDERVMQ LFGLVNTLLA NDPTSLRKNL SIQRYAVIPL ST NSGLIGW VPHCDTLHAL IRDYREKKKI LLNIEHRIML RMAPDYDHLT LMQKVEVFEH AVNNTAGDDL AKLLWLKSPS SEV WFDRRT NYTRSLAVMS MVGYILGLGD RHPSNLMLDR LSGKILHIDF GDCFEVAMTR EKFPEKIPFR LTRMLTNAME VTGL DGNYR ITCHTVMEVL REHKDSVMAV LEAFVYDPLL NWRLMDTNTK GNKRSRTRTD SYSAGQSVEI LDGVELGEPA HKKTG TTVP ESIHSFIGDG LVKPEALNKK AIQIINRVRD KLTGRDFSHD DTLDVPTQVE LLIKQATSHE NLCQCYIGWC PFW

UniProtKB: Serine/threonine-protein kinase mTOR

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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: Homo sapiens (human)
Molecular weightTheoretical: 35.91009 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #3: Regulatory-associated protein of mTOR

MacromoleculeName: Regulatory-associated protein of mTOR / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150.197 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKE SEMLQSPLLG LGEEDEADLT DWNLPLAFMK KRHCEKIEGS KSLAQSWRMK DRMKTVSVAL VLCLNVGVDP PDVVKTTPC ARLECWIDPL SMGPQKALET IGANLQKQYE NWQPRARYKQ SLDPTVDEVK KLCTSLRRNA KEERVLFHYN G HGVPRPTV ...String:
MDYKDDDDKE SEMLQSPLLG LGEEDEADLT DWNLPLAFMK KRHCEKIEGS KSLAQSWRMK DRMKTVSVAL VLCLNVGVDP PDVVKTTPC ARLECWIDPL SMGPQKALET IGANLQKQYE NWQPRARYKQ SLDPTVDEVK KLCTSLRRNA KEERVLFHYN G HGVPRPTV NGEVWVFNKN YTQYIPLSIY DLQTWMGSPS IFVYDCSNAG LIVKSFKQFA LQREQELEVA AINPNHPLAQ MP LPPSMKN CIQLAACEAT ELLPMIPDLP ADLFTSCLTT PIKIALRWFC MQKCVSLVPG VTLDLIEKIP GRLNDRRTPL GEL NWIFTA ITDTIAWNVL PRDLFQKLFR QDLLVASLFR NFLLAERIMR SYNCTPVSSP RLPPTYMHAM WQAWDLAVDI CLSQ LPTII EEGTAFRHSP FFAEQLTAFQ VWLTMGVENR NPPEQLPIVL QVLLSQVHRL RALDLLGRFL DLGPWAVSLA LSVGI FPYV LKLLQSSARE LRPLLVFIWA KILAVDSSCQ ADLVKDNGHK YFLSVLADPY MPAEHRTMTA FILAVIVNSY HTGQEA CLQ GNLIAICLEQ LNDPHPLLRQ WVAICLGRIW QNFDSARWCG VRDSAHEKLY SLLSDPIPEV RCAAVFALGT FVGNSAE RT DHSTTIDHNV AMMLAQLVSD GSPMVRKELV VALSHLVVQY ESNFCTVALQ FIEEEKNYAL PSPATTEGGS LTPVRDSP C TPRLRSVSSY GNIRAVATAR SLNKSLQNLS LTEESGGAVA FSPGNLSTSS SASSTLGSPE NEEHILSFET IDKMRRASS YSSLNSLIGV SFNSVYTQIW RVLLHLAADP YPEVSDVAMK VLNSIAYKAT VNARPQRVLD TSSLTQSAPA SPTNKGVHIH QAGGSPPAS STSSSSLTND VAKQPVSRDL PSGRPGTTGP AGAQYTPHSH QFPRTRKMFD KGPEQTADDA DDAAGHKSFI S ATVQTGFC DWSARYFAQP VMKIPEEHDL ESQIRKEREW RFLRNSRVRR QAQQVIQKGI TRLDDQIFLN RNPGVPSVVK FH PFTPCIA VADKDSICFW DWEKGEKLDY FHNGNPRYTR VTAMEYLNGQ DCSLLLTATD DGAIRVWKNF ADLEKNPEMV TAW QGLSDM LPTTRGAGMV VDWEQETGLL MSSGDVRIVR IWDTDREMKV QDIPTGADSC VTSLSCDSHR SLIVAGLGDG SIRV YDRRM ALSECRVMTY REHTAWVVKA SLQKRPDGHI VSVSVNGDVR IFDPRMPESV NVLQIVKGLT ALDIHPQADL IACGS VNQF TAIYNSSGEL INNIKYYDGF MGQRVGAISC LAFHPHWPHL AVGSNDYYIS VYSVEKRVR

UniProtKB: Regulatory-associated protein of mTOR

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Macromolecule #4: Eukaryotic translation initiation factor 4E-binding protein 1

MacromoleculeName: Eukaryotic translation initiation factor 4E-binding protein 1
type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.951344 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GSGRMSGGSS CSQTPSRAIP ATRRVVLGDG VQLPPGDYST TPGGTLFSTT PGGTRIIYDR KFLMECRNSP VTKTPPRDLP TIPGVTSPS SDEPPMEASQ SHLRNSPEDK RAGGEESQFE MDI

UniProtKB: Eukaryotic translation initiation factor 4E-binding protein 1

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 56.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 580768

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6bcx:
mTORC1 structure refined to 3.0 angstroms

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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

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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

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