[English] 日本語
Yorodumi
- EMDB-13351: cryo-EM structure of DEPTOR bound to human mTOR complex 1, focuss... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13351
Titlecryo-EM structure of DEPTOR bound to human mTOR complex 1, focussed on one protomer
Map data
Sample
  • Complex: mTORC1 in complex with its regulator DEPTOR
    • 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: DEP domain-containing mTOR-interacting protein
  • Ligand: INOSITOL HEXAKISPHOSPHATEPhytic acid
Function / homology
Function and homology information


negative regulation of TORC2 signaling / regulation of extrinsic apoptotic signaling pathway / 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 / 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 / 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 / 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 / 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 / phosphatidic acid binding / nucleus localization / negative regulation of TOR signaling / 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 / protein kinase inhibitor 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 / positive regulation of autophagy / heart morphogenesis / regulation of cellular response to heat / cytoskeleton organization / cardiac muscle contraction / negative regulation of TORC1 signaling / 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 / response to nutrient levels / post-embryonic development / response to nutrient / negative regulation of autophagy / positive regulation of translation / 14-3-3 protein binding / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Regulation of PTEN gene transcription
Similarity search - Function
DEP domain-containing mTOR-interacting protein, DEP domain 1 / DEP domain-containing mTOR-interacting protein, DEP domain 2 / 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 ...DEP domain-containing mTOR-interacting protein, DEP domain 1 / DEP domain-containing mTOR-interacting protein, DEP domain 2 / 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 / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP 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 / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / G-protein beta WD-40 repeat / Winged helix DNA-binding domain superfamily / 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 / Winged helix-like DNA-binding domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase mTOR / Regulatory-associated protein of mTOR / DEP domain-containing mTOR-interacting protein / Target of rapamycin complex subunit LST8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsWaelchli M / Maier T
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation179323 Switzerland
CitationJournal: Elife / Year: 2021
Title: Regulation of human mTOR complexes by DEPTOR.
Authors: Matthias Wälchli / Karolin Berneiser / Francesca Mangia / Stefan Imseng / Louise-Marie Craigie / Edward Stuttfeld / Michael N Hall / Timm Maier /
Abstract: The vertebrate-specific DEP domain-containing mTOR interacting protein (DEPTOR), an oncoprotein or tumor suppressor, has important roles in metabolism, immunity, and cancer. It is the only protein ...The vertebrate-specific DEP domain-containing mTOR interacting protein (DEPTOR), an oncoprotein or tumor suppressor, has important roles in metabolism, immunity, and cancer. It is the only protein that binds and regulates both complexes of mammalian target of rapamycin (mTOR), a central regulator of cell growth. Biochemical analysis and cryo-EM reconstructions of DEPTOR bound to human mTOR complex 1 (mTORC1) and mTORC2 reveal that both structured regions of DEPTOR, the PDZ domain and the DEP domain tandem (DEPt), are involved in mTOR interaction. The PDZ domain binds tightly with mildly activating effect, but then acts as an anchor for DEPt association that allosterically suppresses mTOR activation. The binding interfaces of the PDZ domain and DEPt also support further regulation by other signaling pathways. A separate, substrate-like mode of interaction for DEPTOR phosphorylation by mTOR complexes rationalizes inhibition of non-stimulated mTOR activity at higher DEPTOR concentrations. The multifaceted interplay between DEPTOR and mTOR provides a basis for understanding the divergent roles of DEPTOR in physiology and opens new routes for targeting the mTOR-DEPTOR interaction in disease.
History
DepositionAug 9, 2021-
Header (metadata) releaseSep 8, 2021-
Map releaseSep 8, 2021-
UpdateSep 29, 2021-
Current statusSep 29, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.121
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.121
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7peb
  • Surface level: 0.121
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7peb
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13351.png

Downloads & links

-
Map

FileDownload / File: emd_13351.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.112 Å
Density
Contour LevelBy AUTHOR: 0.121 / Movie #1: 0.121
Minimum - Maximum-0.30343252 - 0.94520694
Average (Standard dev.)-1.2212448e-05 (±0.012969207)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 533.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1121.1121.112
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z533.760533.760533.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.3030.945-0.000

-
Supplemental data

-
Mask #1

Fileemd_13351_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : mTORC1 in complex with its regulator DEPTOR

EntireName: mTORC1 in complex with its regulator DEPTOR
Components
  • Complex: mTORC1 in complex with its regulator DEPTOR
    • 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: DEP domain-containing mTOR-interacting protein
  • Ligand: INOSITOL HEXAKISPHOSPHATEPhytic acid

-
Supramolecule #1: mTORC1 in complex with its regulator DEPTOR

SupramoleculeName: mTORC1 in complex with its regulator DEPTOR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 1.04 MDa

-
Macromolecule #1: Serine/threonine-protein kinase mTOR

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 287.484156 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 ESTRFYDQLN HHIFELVSSS DANERKGGIL AIASLIGVEG GNATRIGRFA NYLRNLLPS NDPVVMEMAS KAIGRLAMAG DTFTAEYVEF EVKRALEWLG ADRNEGRRHA AVLVLRELAI SVPTFFFQQV Q PFFDNIFV AVWDPKQAIR EGAVAALRAC LILTTQREPK EMQKPQWYRH TFEEAEKGFD ETLAKEKGMN RDDRIHGALL IL NELVRIS SMEGERLREE MEEITQQQLV HDKYCKDLMG FGTKPRHITP FTSFQAVQPQ QSNALVGLLG YSSHQGLMGF GTS PSPAKS 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 NLLPRLAAFR PS AFTDTQY LQDTMNHVLS CVKKEKERTA AFQALGLLSV AVRSEFKVYL PRVLDIIRAA LPPKDFAHKR QKAMQVDATV FTC ISMLAR AMGPGIQQDI KELLEPMLAV GLSPALTAVL YDLSRQIPQL KKDIQDGLLK MLSLVLMHKP LRHPGMPKGL AHQL ASPGL TTLPEASDVG SITLALRTLG SFEFEGHSLT QFVRHCADHF LNSEHKEIRM EAARTCSRLL TPSIHLISGH AHVVS QTAV QVVADVLSKL LVVGITDPDP DIRYCVLASL DERFDAHLAQ AENLQALFVA LNDQVFEIRE LAICTVGRLS SMNPAF VMP FLRKMLIQIL TELEHSGIGR IKEQSARMLG HLVSNAPRLI RPYMEPILKA LILKLKDPDP DPNPGVINNV LATIGEL AQ VSGLEMRKWV DELFIIIMDM LQDSSLLAKR QVALWTLGQL VASTGYVVEP YRKYPTLLEV LLNFLKTEQN QGTRREAI R VLGLLGALDP YKHKVNIGMI DQSRDASAVS LSESKSSQDS SDYSTSEMLV NMGNLPLDEF YPAVSMVALM RIFRDQSLS HHHTMVVQAI TFIFKSLGLK CVQFLPQVMP TFLNVIRVCD GAIREFLFQQ LGMLVSFVKS HIRPYMDEIV TLMREFWVMN TSIQSTIIL LIEQIVVALG GEFKLYLPQL IPHMLRVFMH DNSPGRIVSI KLLAAIQLFG ANLDDYLHLL LPPIVKLFDA P EAPLPSRK AALETVDRLT ESLDFTDYAS RIIHPIVRTL DQSPELRSTA MDTLSSLVFQ LGKKYQIFIP MVNKVLVRHR IN HQRYDVL ICRIVKGYTL ADEEEDPLIY QHRMLRSGQG DALASGPVET GPMKKLHVST INLQKAWGAA RRVSKDDWLE WLR RLSLEL LKDSSSPSLR SCWALAQAYN PMARDLFNAA FVSCWSELNE DQQDELIRSI ELALTSQDIA EVTQTLLNLA EFME HSDKG PLPLRDDNGI VLLGERAAKC RAYAKALHYK ELEFQKGPTP AILESLISIN NKLQQPEAAA GVLEYAMKHF GELEI QATW YEKLHEWEDA LVAYDKKMDT NKDDPELMLG RMRCLEALGE WGQLHQQCCE KWTLVNDETQ AKMARMAAAA AWGLGQ WDS MEEYTCMIPR DTHDGAFYRA VLALHQDLFS LAQQCIDKAR DLLDAELTAM AGESYSRAYG AMVSCHMLSE LEEVIQY KL VPERREIIRQ IWWERLQGCQ RIVEDWQKIL MVRSLVVSPH EDMRTWLKYA SLCGKSGRLA LAHKTLVLLL GVDPSRQL D HPLPTVHPQV TYAYMKNMWK SARKIDAFQH MQHFVQTMQQ QAQHAIATED QQHKQELHKL MARCFLKLGE WQLNLQGIN ESTIPKVLQY YSAATEHDRS WYKAWHAWAV MNFEAVLHYK HQNQARDEKK KLRHASGANI TNATTAATTA ATATTTASTE GSNSESEAE STENSPTPSP LQKKVTEDLS KTLLMYTVPA VQGFFRSISL SRGNNLQDTL RVLTLWFDYG HWPDVNEALV E GVKAIQID TWLQVIPQLI ARIDTPRPLV GRLIHQLLTD IGRYHPQALI YPLTVASKST TTARHNAANK ILKNMCEHSN TL VQQAMMV SEELIRVAIL WHEMWHEGLE EASRLYFGER NVKGMFEVLE PLHAMMERGP QTLKETSFNQ AYGRDLMEAQ EWC RKYMKS GNVKDLTQAW DLYYHVFRRI SKQLPQLTSL ELQYVSPKLL MCRDLELAVP GTYDPNQPII RIQSIAPSLQ VITS KQRPR KLTLMGSNGH EFVFLLKGHE DLRQDERVMQ LFGLVNTLLA NDPTSLRKNL SIQRYAVIPL STNSGLIGWV PHCDT LHAL IRDYREKKKI LLNIEHRIML RMAPDYDHLT LMQKVEVFEH AVNNTAGDDL AKLLWLKSPS SEVWFDRRTN YTRSLA VMS MVGYILGLGD RHPSNLMLDR LSGKILHIDF GDCFEVAMTR EKFPEKIPFR LTRMLTNAME VTGLDGNYRI TCHTVME VL REHKDSVMAV LEAFVYDPLL NWRLMDTNTK GNKRSRTRTD SYSAGQSVEI LDGVELGEPA HKKTGTTVPE SIHSFIGD G LVKPEALNKK AIQIINRVRD KLTGRDFSHD DTLDVPTQVE LLIKQATSHE NLCQCYIGWC PFW

-
Macromolecule #2: Target of rapamycin complex subunit LST8

MacromoleculeName: Target of rapamycin complex subunit LST8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.91009 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

-
Macromolecule #3: Regulatory-associated protein of mTOR

MacromoleculeName: Regulatory-associated protein of mTOR / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 155.963094 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAHHHHHHHH HHGSTSGSGE QKLISEEDLG STSGSGDYKD DDDKLTSLYK KAGLENLYFQ GMESEMLQSP LLGLGEEDEA DLTDWNLPL AFMKKRHCEK IEGSKSLAQS WRMKDRMKTV SVALVLCLNV GVDPPDVVKT TPCARLECWI DPLSMGPQKA L ETIGANLQ ...String:
MAHHHHHHHH HHGSTSGSGE QKLISEEDLG STSGSGDYKD DDDKLTSLYK KAGLENLYFQ GMESEMLQSP LLGLGEEDEA DLTDWNLPL AFMKKRHCEK IEGSKSLAQS WRMKDRMKTV SVALVLCLNV GVDPPDVVKT TPCARLECWI DPLSMGPQKA L ETIGANLQ KQYENWQPRA RYKQSLDPTV DEVKKLCTSL RRNAKEERVL FHYNGHGVPR PTVNGEVWVF NKNYTQYIPL SI YDLQTWM GSPSIFVYDC SNAGLIVKSF KQFALQREQE LEVAAINPNH PLAQMPLPPS MKNCIQLAAC EATELLPMIP DLP ADLFTS CLTTPIKIAL RWFCMQKCVS LVPGVTLDLI EKIPGRLNDR RTPLGELNWI FTAITDTIAW NVLPRDLFQK LFRQ DLLVA SLFRNFLLAE RIMRSYNCTP VSSPRLPPTY MHAMWQAWDL AVDICLSQLP TIIEEGTAFR HSPFFAEQLT AFQVW LTMG VENRNPPEQL PIVLQVLLSQ VHRLRALDLL GRFLDLGPWA VSLALSVGIF PYVLKLLQSS ARELRPLLVF IWAKIL AVD SSCQADLVKD NGHKYFLSVL ADPYMPAEHR TMTAFILAVI VNSYHTGQEA CLQGNLIAIC LEQLNDPHPL LRQWVAI CL GRIWQNFDSA RWCGVRDSAH EKLYSLLSDP IPEVRCAAVF ALGTFVGNSA ERTDHSTTID HNVAMMLAQL VSDGSPMV R KELVVALSHL VVQYESNFCT VALQFIEEEK NYALPSPATT EGGSLTPVRD SPCTPRLRSV SSYGNIRAVA TARSLNKSL QNLSLTEESG GAVAFSPGNL STSSSASSTL GSPENEEHIL SFETIDKMRR ASSYSSLNSL IGVSFNSVYT QIWRVLLHLA ADPYPEVSD VAMKVLNSIA YKATVNARPQ RVLDTSSLTQ SAPASPTNKG VHIHQAGGSP PASSTSSSSL TNDVAKQPVS R DLPSGRPG TTGPAGAQYT PHSHQFPRTR KMFDKGPEQT ADDADDAAGH KSFISATVQT GFCDWSARYF AQPVMKIPEE HD LESQIRK EREWRFLRNS RVRRQAQQVI QKGITRLDDQ IFLNRNPGVP SVVKFHPFTP CIAVADKDSI CFWDWEKGEK LDY FHNGNP RYTRVTAMEY LNGQDCSLLL TATDDGAIRV WKNFADLEKN PEMVTAWQGL SDMLPTTRGA GMVVDWEQET GLLM SSGDV RIVRIWDTDR EMKVQDIPTG ADSCVTSLSC DSHRSLIVAG LGDGSIRVYD RRMALSECRV MTYREHTAWV VKASL QKRP DGHIVSVSVN GDVRIFDPRM PESVNVLQIV KGLTALDIHP QADLIACGSV NQFTAIYNSS GELINNIKYY DGFMGQ RVG AISCLAFHPH WPHLAVGSND YYISVYSVEK RVR

-
Macromolecule #4: DEP domain-containing mTOR-interacting protein

MacromoleculeName: DEP domain-containing mTOR-interacting protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.365832 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

-
Macromolecule #5: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE / Phytic acid

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chloridesodium chloride
20.0 mMbicine
5.0 mMMgCl2magnesium chloride
2.0 mMTCEP
0.25 %glycerol
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2

-
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3.2.0)
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 3.2.0)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 3.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 850152

-
Atomic model buiding 1

Initial modelPDB ID:

6bcx

Output model

PDB-7peb:
cryo-EM structure of DEPTOR bound to human mTOR complex 1, focussed on one protomer

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more