[English] 日本語
Yorodumi
- EMDB-11488: cryo-EM structure of human mTOR complex 2, overall refinement -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11488
Titlecryo-EM structure of human mTOR complex 2, overall refinement
Map data
Sample
  • Complex: human mTOR complex 2
    • Protein or peptide: Serine/threonine-protein kinase mTOR
    • Protein or peptide: Target of rapamycin complex subunit LST8
    • Protein or peptide: Rapamycin-insensitive companion of mTOR
  • Protein or peptide: Target of rapamycin complex 2 subunit MAPKAP1
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: ACETYL GROUP
KeywordsmTOR / Kinase / Complex / Inositol / TRANSFERASE
Function / homology
Function and homology information


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 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / TORC2 complex ...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 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / 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 / regulation of cellular response to oxidative stress / calcineurin-NFAT signaling cascade / voluntary musculoskeletal movement / regulation of osteoclast differentiation / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / regulation of lysosome organization / phosphatidic acid binding / 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 / negative regulation of Ras protein signal transduction / phosphatidylinositol-3,4-bisphosphate binding / cellular response to methionine / positive regulation of ubiquitin-dependent protein catabolic process / inositol hexakisphosphate binding / cellular response to osmotic stress / phosphatidylinositol-3,5-bisphosphate binding / negative regulation of protein localization to nucleus / anoikis / embryo development ending in birth or egg hatching / enzyme-substrate adaptor activity / cardiac muscle cell development / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / regulation of establishment of cell polarity / positive regulation of transcription by RNA polymerase III / positive regulation of actin filament polymerization / regulation of cell size / negative regulation of macroautophagy / lipid biosynthetic process / Macroautophagy / positive regulation of myotube differentiation / Constitutive Signaling by AKT1 E17K in Cancer / oligodendrocyte differentiation / germ cell development / behavioral response to pain / phosphatidylinositol-3,4,5-trisphosphate binding / TOR signaling / mTORC1-mediated signalling / CD28 dependent PI3K/Akt signaling / positive regulation of oligodendrocyte differentiation / positive regulation of translational initiation / response to amino acid / positive regulation of TOR signaling / 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 / negative regulation of insulin receptor signaling pathway / positive regulation of stress fiber assembly / phagocytic vesicle / cytoskeleton organization / T cell costimulation / positive regulation of endothelial cell proliferation / phosphatidylinositol-4,5-bisphosphate binding / substantia nigra development / positive regulation of peptidyl-tyrosine phosphorylation / endomembrane system / negative regulation of autophagy / cellular response to amino acid starvation / protein serine/threonine kinase activator activity / positive regulation of glycolytic process / post-embryonic development / cellular response to starvation / Regulation of PTEN gene transcription / regulation of signal transduction by p53 class mediator
Similarity search - Function
Rapamycin-insensitive companion of mTOR, N-terminal domain / Pianissimo family / Rapamycin-insensitive companion of mTOR, phosphorylation-site / Rapamycin-insensitive companion of mTOR, middle domain / Rapamycin-insensitive companion of mTOR, domain 5 / Rapamycin-insensitive companion of mTOR, domain 4 / Rapamycin-insensitive companion of mTOR RasGEF_N domain / Rapamycin-insensitive companion of mTOR, N-term / Rapamycin-insensitive companion of mTOR, phosphorylation-site / Rapamycin-insensitive companion of mTOR, middle domain ...Rapamycin-insensitive companion of mTOR, N-terminal domain / Pianissimo family / Rapamycin-insensitive companion of mTOR, phosphorylation-site / Rapamycin-insensitive companion of mTOR, middle domain / Rapamycin-insensitive companion of mTOR, domain 5 / Rapamycin-insensitive companion of mTOR, domain 4 / Rapamycin-insensitive companion of mTOR RasGEF_N domain / Rapamycin-insensitive companion of mTOR, N-term / Rapamycin-insensitive companion of mTOR, phosphorylation-site / Rapamycin-insensitive companion of mTOR, middle domain / Rapamycin-insensitive companion of mTOR, domain 5 / Rapamycin-insensitive companion of mTOR RasGEF_N domain / Rapamycin-insensitive companion of mTOR, middle domain / Rapamycin-insensitive companion of mTOR, N-term / Rapamycin-insensitive companion of mTOR, phosphorylation-site / Rapamycin-insensitive companion of mTOR, domain 5 / Sin1, N-terminal / Stress-activated map kinase interacting protein 1 (SIN1) / TORC2 component Sin1/Avo1 / SAPK-interacting protein 1, Pleckstrin-homology domain / Sin1, middle CRIM domain / SAPK-interacting protein 1 (Sin1), middle CRIM domain / SAPK-interacting protein 1 (Sin1), Pleckstrin-homology / 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 / : / 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. / 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 / PH-like 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/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase mTOR / Rapamycin-insensitive companion of mTOR / Target of rapamycin complex 2 subunit MAPKAP1 / Target of rapamycin complex subunit LST8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsScaiola A / Mangia F
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation179323 Switzerland
Swiss National Science Foundation177084 Switzerland
Swiss National Science Foundation138262
CitationJournal: Sci Adv / Year: 2020
Title: The 3.2-Å resolution structure of human mTORC2.
Authors: Alain Scaiola / Francesca Mangia / Stefan Imseng / Daniel Boehringer / Karolin Berneiser / Mitsugu Shimobayashi / Edward Stuttfeld / Michael N Hall / Nenad Ban / Timm Maier /
Abstract: The protein kinase mammalian target of rapamycin (mTOR) is the central regulator of cell growth. Aberrant mTOR signaling is linked to cancer, diabetes, and neurological disorders. mTOR exerts its ...The protein kinase mammalian target of rapamycin (mTOR) is the central regulator of cell growth. Aberrant mTOR signaling is linked to cancer, diabetes, and neurological disorders. mTOR exerts its functions in two distinct multiprotein complexes, mTORC1 and mTORC2. Here, we report a 3.2-Å resolution cryo-EM reconstruction of mTORC2. It reveals entangled folds of the defining Rictor and the substrate-binding SIN1 subunits, identifies the carboxyl-terminal domain of Rictor as the source of the rapamycin insensitivity of mTORC2, and resolves mechanisms for mTORC2 regulation by complex destabilization. Two previously uncharacterized small-molecule binding sites are visualized, an inositol hexakisphosphate (InsP6) pocket in mTOR and an mTORC2-specific nucleotide binding site in Rictor, which also forms a zinc finger. Structural and biochemical analyses suggest that InsP6 and nucleotide binding do not control mTORC2 activity directly but rather have roles in folding or ternary interactions. These insights provide a firm basis for studying mTORC2 signaling and for developing mTORC2-specific inhibitors.
History
DepositionJul 28, 2020-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.375
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.375
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6zwm
  • Surface level: 0.375
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11488.png

Downloads & links

-
Map

FileDownload / File: emd_11488.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 320 pix.
= 430.08 Å		1.34 Å/pix.
x 320 pix.
= 430.08 Å		1.34 Å/pix.
x 320 pix.
= 430.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.344 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.375 / Movie #1: 0.375
Minimum - Maximum-1.7557929 - 3.3231337
Average (Standard dev.)-0.0021909792 (±0.07714291)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 430.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3441.3441.344
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z430.080430.080430.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.7563.323-0.002

-
Supplemental data

-
Mask #1

Fileemd_11488_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_11488_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_11488_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_11488_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : human mTOR complex 2

EntireName: human mTOR complex 2
Components
  • Complex: human mTOR complex 2
    • Protein or peptide: Serine/threonine-protein kinase mTOR
    • Protein or peptide: Target of rapamycin complex subunit LST8
    • Protein or peptide: Rapamycin-insensitive companion of mTOR
  • Protein or peptide: Target of rapamycin complex 2 subunit MAPKAP1
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: ACETYL GROUP

-
Supramolecule #1: human mTOR complex 2

SupramoleculeName: human mTOR complex 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.15 MDa

-
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: 289.257969 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MLGTGPAAAT TAATTSSNVS VLQQFASGLK SRNEETRAKA AKELQHYVTM ELREMSQEES TRFYDQLNHH IFELVSSSDA NERKGGILA IASLIGVEGG NATRIGRFAN YLRNLLPSND PVVMEMASKA IGRLAMAGDT FTAEYVEFEV KRALEWLGAD R NEGRRHAA ...String:
MLGTGPAAAT TAATTSSNVS VLQQFASGLK SRNEETRAKA AKELQHYVTM ELREMSQEES TRFYDQLNHH IFELVSSSDA NERKGGILA IASLIGVEGG NATRIGRFAN YLRNLLPSND PVVMEMASKA IGRLAMAGDT FTAEYVEFEV KRALEWLGAD R NEGRRHAA VLVLRELAIS VPTFFFQQVQ PFFDNIFVAV WDPKQAIREG AVAALRACLI LTTQREPKEM QKPQWYRHTF EE AEKGFDE TLAKEKGMNR DDRIHGALLI LNELVRISSM EGERLREEME EITQQQLVHD KYCKDLMGFG TKPRHITPFT SFQ AVQPQQ SNALVGLLGY SSHQGLMGFG TSPSPAKSTL VESRCCRDLM EEKFDQVCQW VLKCRNSKNS LIQMTILNLL PRLA AFRPS AFTDTQYLQD TMNHVLSCVK KEKERTAAFQ ALGLLSVAVR SEFKVYLPRV LDIIRAALPP KDFAHKRQKA MQVDA TVFT CISMLARAMG PGIQQDIKEL LEPMLAVGLS PALTAVLYDL SRQIPQLKKD IQDGLLKMLS LVLMHKPLRH PGMPKG LAH QLASPGLTTL PEASDVGSIT LALRTLGSFE FEGHSLTQFV RHCADHFLNS EHKEIRMEAA RTCSRLLTPS IHLISGH AH VVSQTAVQVV ADVLSKLLVV GITDPDPDIR YCVLASLDER FDAHLAQAEN LQALFVALND QVFEIRELAI CTVGRLSS M NPAFVMPFLR KMLIQILTEL EHSGIGRIKE QSARMLGHLV SNAPRLIRPY MEPILKALIL KLKDPDPDPN PGVINNVLA TIGELAQVSG LEMRKWVDEL FIIIMDMLQD SSLLAKRQVA LWTLGQLVAS TGYVVEPYRK YPTLLEVLLN FLKTEQNQGT RREAIRVLG LLGALDPYKH KVNIGMIDQS RDASAVSLSE SKSSQDSSDY STSEMLVNMG NLPLDEFYPA VSMVALMRIF R DQSLSHHH TMVVQAITFI FKSLGLKCVQ FLPQVMPTFL NVIRVCDGAI REFLFQQLGM LVSFVKSHIR PYMDEIVTLM RE FWVMNTS IQSTIILLIE QIVVALGGEF KLYLPQLIPH MLRVFMHDNS PGRIVSIKLL AAIQLFGANL DDYLHLLLPP IVK LFDAPE APLPSRKAAL ETVDRLTESL DFTDYASRII HPIVRTLDQS PELRSTAMDT LSSLVFQLGK KYQIFIPMVN KVLV RHRIN HQRYDVLICR IVKGYTLADE EEDPLIYQHR MLRSGQGDAL ASGPVETGPM KKLHVSTINL QKAWGAARRV SKDDW LEWL RRLSLELLKD SSSPSLRSCW ALAQAYNPMA RDLFNAAFVS CWSELNEDQQ DELIRSIELA LTSQDIAEVT QTLLNL AEF MEHSDKGPLP LRDDNGIVLL GERAAKCRAY AKALHYKELE FQKGPTPAIL ESLISINNKL QQPEAAAGVL EYAMKHF GE LEIQATWYEK LHEWEDALVA YDKKMDTNKD DPELMLGRMR CLEALGEWGQ LHQQCCEKWT LVNDETQAKM ARMAAAAA W GLGQWDSMEE YTCMIPRDTH DGAFYRAVLA LHQDLFSLAQ QCIDKARDLL DAELTAMAGE SYSRAYGAMV SCHMLSELE EVIQYKLVPE RREIIRQIWW ERLQGCQRIV EDWQKILMVR SLVVSPHEDM RTWLKYASLC GKSGRLALAH KTLVLLLGVD PSRQLDHPL PTVHPQVTYA YMKNMWKSAR KIDAFQHMQH FVQTMQQQAQ HAIATEDQQH KQELHKLMAR CFLKLGEWQL N LQGINEST IPKVLQYYSA ATEHDRSWYK AWHAWAVMNF EAVLHYKHQN QARDEKKKLR HASGANITNA TTAATTAATA TT TASTEGS NSESEAESTE NSPTPSPLQK KVTEDLSKTL LMYTVPAVQG FFRSISLSRG NNLQDTLRVL TLWFDYGHWP DVN EALVEG VKAIQIDTWL QVIPQLIARI DTPRPLVGRL IHQLLTDIGR YHPQALIYPL TVASKSTTTA RHNAANKILK NMCE HSNTL VQQAMMVSEE LIRVAILWHE MWHEGLEEAS RLYFGERNVK GMFEVLEPLH AMMERGPQTL KETSFNQAYG RDLME AQEW CRKYMKSGNV KDLTQAWDLY YHVFRRISKQ LPQLTSLELQ YVSPKLLMCR DLELAVPGTY DPNQPIIRIQ SIAPSL QVI TSKQRPRKLT LMGSNGHEFV FLLKGHEDLR QDERVMQLFG LVNTLLANDP TSLRKNLSIQ RYAVIPLSTN SGLIGWV PH CDTLHALIRD YREKKKILLN IEHRIMLRMA PDYDHLTLMQ KVEVFEHAVN NTAGDDLAKL LWLKSPSSEV WFDRRTNY T RSLAVMSMVG YILGLGDRHP SNLMLDRLSG KILHIDFGDC FEVAMTREKF PEKIPFRLTR MLTNAMEVTG LDGNYRITC HTVMEVLREH KDSVMAVLEA FVYDPLLNWR LMDTNTKGNK RSRTRTDSYS AGQSVEILDG VELGEPAHKK TGTTVPESIH SFIGDGLVK PEALNKKAIQ IINRVRDKLT GRDFSHDDTL DVPTQVELLI KQATSHENLC QCYIGWCPFW

UniProtKB: Serine/threonine-protein kinase mTOR

-
Macromolecule #2: Target of rapamycin complex subunit LST8

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: 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

UniProtKB: Target of rapamycin complex subunit LST8

-
Macromolecule #3: Rapamycin-insensitive companion of mTOR

MacromoleculeName: Rapamycin-insensitive companion of mTOR / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 192.472922 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAIGRGRSL KNLRVRGRND SGEENVPLDL TREPSDNLRE ILQNVARLQG VSNMRKLGHL NNFTKLLCDI GHSEEKLGFH YEDIIICLR LALLNEAKEV RAAGLRALRY LIQDSSILQK VLKLKVDYLI ARCIDIQQSN EVERTQALRL VRKMITVNAS L FPSSVTNS ...String:
MAAIGRGRSL KNLRVRGRND SGEENVPLDL TREPSDNLRE ILQNVARLQG VSNMRKLGHL NNFTKLLCDI GHSEEKLGFH YEDIIICLR LALLNEAKEV RAAGLRALRY LIQDSSILQK VLKLKVDYLI ARCIDIQQSN EVERTQALRL VRKMITVNAS L FPSSVTNS LIAVGNDGLQ ERDRMVRACI AIICELALQN PEVVALRGGL NTILKNVIDC QLSRINEALI TTILHLLNHP KT RQYVRAD VELERILAPY TDFHYRHSPD TAEGQLKEDR EARFLASKMG IIATFRSWAG IINLCKPGNS GIQSLIGVLC IPN MEIRRG LLEVLYDIFR LPLPVVTEEF IEALLSVDPG RFQDSWRLSD GFVAAEAKTI LPHRARSRPD LMDNYLALIL SAFI RNGLL EGLVEVITNS DDHISVRATI LLGELLHMAN TILPHSHSHH LHCLPTLMNM AASFDIPKEK RLRASAALNC LKRFH EMKK RGPKPYSLHL DHIIQKAIAT HQKRDQYLRV QKDIFILKDT EEALLINLRD SQVLQHKENL EWNWNLIGTI LKWPNV NLR NYKDEQLHRF VRRLLYFYKP SSKLYANLDL DFAKAKQLTV VGCQFTEFLL ESEEDGQGYL EDLVKDIVQW LNASSGM KP ERSLQNNGLL TTLSQHYFLF IGTLSCHPHG VKMLEKCSVF QCLLNLCSLK NQDHLLKLTV SSLDYSRDGL ARVILSKI L TAATDACRLY ATKHLRVLLR ANVEFFNNWG IELLVTQLHD KNKTISSEAL DILDEACEDK ANLHALIQMK PALSHLGDK GLLLLLRFLS IPKGFSYLNE RGYVAKQLEK WHREYNSKYV DLIEEQLNEA LTTYRKPVDG DNYVRRSNQR LQRPHVYLPI HLYGQLVHH KTGCHLLEVQ NIITELCRNV RTPDLDKWEE IKKLKASLWA LGNIGSSNWG LNLLQEENVI PDILKLAKQC E VLSIRGTC VYVLGLIAKT KQGCDILKCH NWDAVRHSRK HLWPVVPDDV EQLCNELSSI PSTLSLNSES TSSRHNSESE SV PSSMFIL EDDRFGSSST STFFLDINED TEPTFYDRSG PIKDKNSFPF FASSKLVKNR ILNSLTLPNK KHRSSSDPKG GKL SSESKT SNRRIRTLTE PSVDFNHSDD FTPISTVQKT LQLETSFMGN KHIEDTGSTP SIGENDLKFT KNFGTENHRE NTSR ERLVV ESSTSSHMKI RSQSFNTDTT TSGISSMSSS PSRETVGVDA TTMDTDCGSM STVVSTKTIK TSHYLTPQSN HLSLS KSNS VSLVPPGSSH TLPRRAQSLK APSIATIKSL ADCNFSYTSS RDAFGYATLK RLQQQRMHPS LSHSEALASP AKDVLF TDT ITMKANSFES RLTPSRFMKA LSYASLDKED LLSPINQNTL QRSSSVRSMV SSATYGGSDD YIGLALPVDI NDIFQVK DI PYFQTKNIPP HDDRGARAFA HDAGGLPSGT GGLVKNSFHL LRQQMSLTEI MNSIHSDASL FLESTEDTGL QEHTDDNC L YCVCIEILGF QPSNQLSAIC SHSDFQDIPY SDWCEQTIHN PLEVVPSKFS GISGCSDGVS QEGSASSTKS TELLLGVKT IPDDTPMCRI LLRKEVLRLV INLSSSVSTK CHETGLLTIK EKYPQTFDDI CLYSEVSHLL SHCTFRLPCR RFIQELFQDV QFLQMHEEA EAVLATPPKQ PIVDTSAES

UniProtKB: Rapamycin-insensitive companion of mTOR

-
Macromolecule #4: Target of rapamycin complex 2 subunit MAPKAP1

MacromoleculeName: Target of rapamycin complex 2 subunit MAPKAP1 / type: protein_or_peptide / ID: 4
Details: MAFLDNPTIILAHIRQSHVTSDDTGMCEMVLIDHDVDLEKIHPPSMPGDSGSEIQGSNGE TQGYVYAQSVDITSSWDFGIRRRSNTAQRLERLRKERQNQIKCKNIQWKERNSKQSAQEL KSLFEKKSLKEKPPISGKQSILSVRLEQCPLQLNNPFNEYSKFDGKGHVGTTATKKIDVY ...Details: MAFLDNPTIILAHIRQSHVTSDDTGMCEMVLIDHDVDLEKIHPPSMPGDSGSEIQGSNGE TQGYVYAQSVDITSSWDFGIRRRSNTAQRLERLRKERQNQIKCKNIQWKERNSKQSAQEL KSLFEKKSLKEKPPISGKQSILSVRLEQCPLQLNNPFNEYSKFDGKGHVGTTATKKIDVY LPLHSSQDRLLPMTVVTMASARVQDLIGLICWQYTSEGREPKLNDNVSAYCLHIAEDDGE VDTDFPPLDSNEPIHKFGFSTLALVEKYSSPGLTSKESLFVRINAAHGFSLIQVDNTKVT MKEILLKAVKRRKGSQKVSGPQYRLEKQSEPNVAVDLDSTLESQSAWEFCLVRENSSRAD GVFEEDSQIDIATVQDMLSSHHYKSFKVSMIHRLRFTTDVQLGISGDKVEIDPVTNQKAS TKFWIKQKPISIDSDLLCACDLAEEKSPSHAIFKLTYLSNHDYKHLYFESDAATVNEIVL KVNYILESRASTARADYFAQKQRKLNRRTSFSFQKEKKSGQQ
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.206738 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAFLDNPTII LAHIRQSHVT SDDTGMCEMV LIDHDVDLEK IHPPSMPGDS GSEIQGSNGE TQGYVYAQSV DITSSWDFGI RRRSNTAQR LERLRKERQN QIKCKNIQWK ERNSKQSAQE LKSLFEKKSL KEKPPISGKQ SILSVRLEQC PLQLNNPFNE Y SKFDGKGH ...String:
MAFLDNPTII LAHIRQSHVT SDDTGMCEMV LIDHDVDLEK IHPPSMPGDS GSEIQGSNGE TQGYVYAQSV DITSSWDFGI RRRSNTAQR LERLRKERQN QIKCKNIQWK ERNSKQSAQE LKSLFEKKSL KEKPPISGKQ SILSVRLEQC PLQLNNPFNE Y SKFDGKGH VGTTATKKID VYLPLHSSQD RLLPMTVVTM ASARVQDLIG LICWQYTSEG REPKLNDNVS AYCLHIAEDD GE VDTDFPP LDSNEPIHKF GFSTLALVEK YSSPGLTSKE SLFVRINAAH GFSLIQVDNT KVTMKEILLK AVKRRKGSQK VSG PQYRLE KQSEPNVAVD LDSTLESQSA WEFCLVRENS SRADGVFEED SQIDIATVQD MLSSHHYKSF KVSMIHRLRF TTDV QLGIS GDKVEIDPVT NQKASTKFWI KQKPISIDSD LLCACDLAEE KSPSHAIFKL TYLSNHDYKH LYFESDAATV NEIVL KVNY ILESRASTAR ADYFAQKQRK LNRRTSFSFQ KEKKSGQQ

UniProtKB: Target of rapamycin complex 2 subunit MAPKAP1

-
Macromolecule #5: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 4 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

-
Macromolecule #6: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

-
Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #8: ACETYL GROUP

MacromoleculeName: ACETYL GROUP / type: ligand / ID: 8 / Number of copies: 2 / Formula: ACE
Molecular weightTheoretical: 44.053 Da
Chemical component information

ChemComp-ACE:
ACETYL GROUP

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.37 mg/mL
BufferpH: 8.5
GridModel: Quantifoil / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 293038
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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