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- EMDB-7086: active dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-7086
Titleactive dimer
Map dataPrimary consensus dimer map in C2.
Sample
  • Complex: active complex
    • Protein or peptide: Serine/threonine-protein kinase mTOR,Serine/threonine-protein kinase mTOR
    • Protein or peptide: Target of rapamycin complex subunit LST8
    • Protein or peptide: Regulatory-associated protein of mTOR,Regulatory-associated protein of mTOR
    • Protein or peptide: Eukaryotic translation initiation factor 4E-binding protein 1
    • Protein or peptide: GTP-binding protein Rheb
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
KeywordsPIKK / TRANSFERASE
Function / homology
Function and homology information


regulation of type B pancreatic cell development / 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 / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / TORC2 signaling ...regulation of type B pancreatic cell development / 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 / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / TORC2 signaling / eukaryotic initiation factor 4E binding / TORC2 complex / regulation of membrane permeability / cellular response to leucine starvation / heart valve morphogenesis / negative regulation of lysosome organization / TFIIIC-class transcription factor complex binding / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / voluntary musculoskeletal movement / regulation of osteoclast differentiation / positive regulation of odontoblast differentiation / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / regulation of lysosome organization / Amino acids regulate mTORC1 / cellular response to L-leucine / MTOR signalling / cellular response to nutrient / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / TORC1 signaling / energy reserve metabolic process / ruffle organization / serine/threonine protein kinase complex / negative regulation of cell size / vascular endothelial cell response to laminar fluid shear stress / cellular response to methionine / positive regulation of osteoclast differentiation / positive regulation of ubiquitin-dependent protein catabolic process / inositol hexakisphosphate binding / cellular response to osmotic stress / negative regulation of protein localization to nucleus / anoikis / protein serine/threonine kinase inhibitor activity / enzyme-substrate adaptor activity / cardiac muscle cell development / negative regulation of cold-induced thermogenesis / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / positive regulation of transcription by RNA polymerase III / positive regulation of actin filament polymerization / regulation of cell size / negative regulation of macroautophagy / small GTPase-mediated signal transduction / Macroautophagy / positive regulation of myotube differentiation / Constitutive Signaling by AKT1 E17K in Cancer / social behavior / oligodendrocyte differentiation / germ cell development / behavioral response to pain / TOR signaling / mTORC1-mediated signalling / CD28 dependent PI3K/Akt signaling / positive regulation of oligodendrocyte differentiation / positive regulation of translational initiation / protein kinase activator activity / response to amino acid / positive regulation of TOR signaling / positive regulation of G1/S transition of mitotic cell cycle / HSF1-dependent transactivation / regulation of macroautophagy / 'de novo' pyrimidine nucleobase biosynthetic process / cellular response to nutrient levels / neuronal action potential / positive regulation of lipid biosynthetic process / positive regulation of epithelial to mesenchymal transition / heart morphogenesis / regulation of cellular response to heat / cardiac muscle contraction / positive regulation of lamellipodium assembly / positive regulation of peptidyl-threonine phosphorylation / positive regulation of stress fiber assembly / phagocytic vesicle / cytoskeleton organization / translation repressor activity / translation initiation factor binding / negative regulation of translational initiation / T cell costimulation / positive regulation of endothelial cell proliferation / 14-3-3 protein binding / positive regulation of TORC1 signaling / endomembrane system / positive regulation of mitotic cell cycle / negative regulation of autophagy / cellular response to amino acid starvation / protein serine/threonine kinase activator activity / positive regulation of peptidyl-serine phosphorylation
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 / Serine/threonine-protein kinase ATR-like, HEAT repeats / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain ...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 / Serine/threonine-protein kinase ATR-like, HEAT repeats / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / HEAT repeat / HEAT repeat / : / FATC domain / PIK-related kinase, FAT / FAT 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. / Small GTPase, Ras-type / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / small GTPase Ras family profile. / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / 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 / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Serine/threonine-protein kinase mTOR / Eukaryotic translation initiation factor 4E-binding protein 1 / GTP-binding protein Rheb / Regulatory-associated protein of mTOR / Target of rapamycin complex subunit LST8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6bcu
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7086.png

Downloads & links

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Map

FileDownload / File: emd_7086.map.gz / Format: CCP4 / Size: 199.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary consensus dimer map in C2.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 374 pix.
= 497.644 Å		1.33 Å/pix.
x 374 pix.
= 497.644 Å		1.33 Å/pix.
x 374 pix.
= 497.644 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3306 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.08613933 - 0.16707982
Average (Standard dev.)-0.00005109722 (±0.0039210147)
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-0.0860.167-0.000

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Supplemental data

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

Fileemd_7086_additional_1.map
AnnotationFocused 3D refinement of monomer part2 (mask 2) used to reconstruct the 3.4 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 part1 (mask 1)...

Fileemd_7086_additional_2.map
AnnotationFocused 3D refinement of monomer part1 (mask 1) used to reconstruct the 3.4 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_7086_additional_3.map
AnnotationFocused 3D refinement of monomer part3 (mask 3) used to reconstruct the 3.4 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 : active complex

EntireName: active complex
Components
  • Complex: active complex
    • Protein or peptide: Serine/threonine-protein kinase mTOR,Serine/threonine-protein kinase mTOR
    • Protein or peptide: Target of rapamycin complex subunit LST8
    • Protein or peptide: Regulatory-associated protein of mTOR,Regulatory-associated protein of mTOR
    • Protein or peptide: Eukaryotic translation initiation factor 4E-binding protein 1
    • Protein or peptide: GTP-binding protein Rheb
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: active complex

SupramoleculeName: active complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serine/threonine-protein kinase mTOR,Serine/threonine-protein kin...

MacromoleculeName: Serine/threonine-protein kinase mTOR,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,Regulatory-associated prote...

MacromoleculeName: Regulatory-associated protein of mTOR,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, 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: GTP-binding protein Rheb

MacromoleculeName: GTP-binding protein Rheb / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.877826 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GSGRMPQSKS RKIAILGYRS VGKSSLTIQF VEGQFVDSYD PTIENTFTKL ITVNGQEYHL QLVDTAGQDE YSIFPQTYSI DINGYILVY SVTSIKSFEV IKVIHGKLLD MVGKVQIPIM LVGNKKDLHM ERVISYEEGK ALAESWNAAF LESSAKENQT A VDVFRRII LEAEKMDGAA SQGKSSCSVM

UniProtKB: GTP-binding protein Rheb

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 198237
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6bcu:
Cryo-EM structure of the activated RHEB-mTORC1 refined to 3.4 angstrom

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