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- EMDB-55803: cryo-EM structure of dephosphorylated mTOR complex 2, overall ref... -

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Basic information

Entry
Database: EMDB / ID: EMD-55803
Titlecryo-EM structure of dephosphorylated mTOR complex 2, overall refinement
Map data
Sample
  • Complex: mTOR complex 2, dephosphorylated
    • 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: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ZINC ION
KeywordsKinase / Complex / Signaling protein / TRANSFERASE
Function / homology
Function and homology information


positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process / 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 / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / regulation of membrane permeability / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction ...positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process / 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 / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / regulation of membrane permeability / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / TORC2 complex / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / heart valve morphogenesis / voluntary musculoskeletal movement / negative regulation of lysosome organization / TORC1 complex / regulation of cellular response to oxidative stress / calcineurin-NFAT signaling cascade / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / regulation of osteoclast differentiation / MTOR signalling / energy reserve metabolic process / regulation of lysosome organization / cellular response to L-leucine / Energy dependent regulation of mTOR by LKB1-AMPK / cellular response to nutrient / regulation of autophagosome assembly / Amino acids regulate mTORC1 / phosphatidic acid binding / negative regulation of Ras protein signal transduction / cellular response to methionine / embryo development ending in birth or egg hatching / phosphatidylinositol-3,4-bisphosphate binding / negative regulation of cell size / TORC2 signaling / cellular response to osmotic stress / phosphatidylinositol-3,5-bisphosphate binding / cell projection organization / anoikis / inositol hexakisphosphate binding / cardiac muscle cell development / negative regulation of calcineurin-NFAT signaling cascade / positive regulation of ubiquitin-dependent protein catabolic process / regulation of myelination / negative regulation of protein localization to nucleus / positive regulation of transcription by RNA polymerase III / positive regulation of ruffle assembly / regulation of cell size / positive regulation of myotube differentiation / lipid biosynthetic process / negative regulation of macroautophagy / regulation of establishment of cell polarity / Macroautophagy / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of actin filament polymerization / germ cell development / oligodendrocyte differentiation / phosphatidylinositol-3,4,5-trisphosphate binding / TORC1 signaling / positive regulation of oligodendrocyte differentiation / behavioral response to pain / response to amino acid / positive regulation of translational initiation / TOR signaling / mTORC1-mediated signalling / CD28 dependent PI3K/Akt signaling / HSF1-dependent transactivation / regulation of macroautophagy / positive regulation of TOR signaling / enzyme-substrate adaptor activity / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of epithelial to mesenchymal transition / positive regulation of lipid biosynthetic process / vascular endothelial cell response to laminar fluid shear stress / heart morphogenesis / regulation of cellular response to heat / positive regulation of lamellipodium assembly / neuronal action potential / T cell costimulation / phagocytic vesicle / positive regulation of stress fiber assembly / cardiac muscle contraction / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of endothelial cell proliferation / negative regulation of insulin receptor signaling pathway / cytoskeleton organization / endomembrane system / substantia nigra development / cellular response to nutrient levels / positive regulation of glycolytic process / cellular response to amino acid starvation / cellular response to starvation / Regulation of PTEN gene transcription / regulation of signal transduction by p53 class mediator / negative regulation of autophagy / VEGFR2 mediated vascular permeability / protein serine/threonine kinase activator activity
Similarity search - Function
Rapamycin-insensitive companion of mTOR, phosphorylation-site / Rapamycin-insensitive companion of mTOR, phosphorylation-site / Rapamycin-insensitive companion of mTOR, phosphorylation-site / Rapamycin-insensitive companion of mTOR, N-terminal domain / Pianissimo family / 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, phosphorylation-site / Rapamycin-insensitive companion of mTOR, phosphorylation-site / Rapamycin-insensitive companion of mTOR, N-terminal domain / Pianissimo family / 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, 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, domain 5 / : / SIN1 Ras-binding domain / 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 / 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 / : / Serine/threonine-protein kinase ATR-like, HEAT repeats / : / 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 / PH-like domain superfamily / Tetratricopeptide-like helical domain superfamily / WD domain, G-beta repeat / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / 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: 3.3 Å
AuthorsHay IM / Anandapadamanaban M / Williams RL
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Biorxiv / Year: 2026
Title: Structural basis for a phosphoinositide-driven mTORC2-AKT positive feedback loop
Authors: Hay IM / Bourguet M / Ahsan B / Perisic O / Anandapadamanaban M / Williams RL
History
DepositionNov 24, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55803.png

Downloads & links

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Map

FileDownload / File: emd_55803.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 512 pix.
= 488.96 Å		0.96 Å/pix.
x 512 pix.
= 488.96 Å		0.96 Å/pix.
x 512 pix.
= 488.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.955 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.0027327798 - 0.030550424
Average (Standard dev.)0.00042522186 (±0.00075968733)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 488.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_55803_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mTOR complex 2, dephosphorylated

EntireName: mTOR complex 2, dephosphorylated
Components
  • Complex: mTOR complex 2, dephosphorylated
    • 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: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: mTOR complex 2, dephosphorylated

SupramoleculeName: mTOR complex 2, dephosphorylated / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: mTOR complex 2 dephosphorylated in vitro with lambda protein phosphatase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 580 KDa

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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: 293.557656 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGENLYFQGG TMLGTGPAAA TTAATTSSNV SVLQQFASGL KSRNEETRAK AAKELQHYV TMELREMSQE ESTRFYDQLN HHIFELVSSS DANERKGGIL AIASLIGVEG GNATRIGRFA NYLRNLLPSN D PVVMEMAS ...String:
MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGENLYFQGG TMLGTGPAAA TTAATTSSNV SVLQQFASGL KSRNEETRAK AAKELQHYV TMELREMSQE ESTRFYDQLN HHIFELVSSS DANERKGGIL AIASLIGVEG GNATRIGRFA NYLRNLLPSN D PVVMEMAS KAIGRLAMAG DTFTAEYVEF EVKRALEWLG ADRNEGRRHA AVLVLRELAI SVPTFFFQQV QPFFDNIFVA VW DPKQAIR EGAVAALRAC LILTTQREPK EMQKPQWYRH TFEEAEKGFD ETLAKEKGMN RDDRIHGALL ILNELVRISS MEG ERLREE MEEITQQQLV HDKYCKDLMG FGTKPRHITP FTSFQAVQPQ QSNALVGLLG YSSHQGLMGF GTSPSPAKST LVES RCCRD LMEEKFDQVC QWVLKCRNSK NSLIQMTILN LLPRLAAFRP SAFTDTQYLQ DTMNHVLSCV KKEKERTAAF QALGL LSVA VRSEFKVYLP RVLDIIRAAL PPKDFAHKRQ KAMQVDATVF TCISMLARAM GPGIQQDIKE LLEPMLAVGL SPALTA VLY DLSRQIPQLK KDIQDGLLKM LSLVLMHKPL RHPGMPKGLA HQLASPGLTT LPEASDVGSI TLALRTLGSF EFEGHSL TQ FVRHCADHFL NSEHKEIRME AARTCSRLLT PSIHLISGHA HVVSQTAVQV VADVLSKLLV VGITDPDPDI RYCVLASL D ERFDAHLAQA ENLQALFVAL NDQVFEIREL AICTVGRLSS MNPAFVMPFL RKMLIQILTE LEHSGIGRIK EQSARMLGH LVSNAPRLIR PYMEPILKAL ILKLKDPDPD PNPGVINNVL ATIGELAQVS GLEMRKWVDE LFIIIMDMLQ DSSLLAKRQV ALWTLGQLV ASTGYVVEPY RKYPTLLEVL LNFLKTEQNQ GTRREAIRVL GLLGALDPYK HKVNIGMIDQ SRDASAVSLS E SKSSQDSS DYSTSEMLVN MGNLPLDEFY PAVSMVALMR IFRDQSLSHH HTMVVQAITF IFKSLGLKCV QFLPQVMPTF LN VIRVCDG AIREFLFQQL GMLVSFVKSH IRPYMDEIVT LMREFWVMNT SIQSTIILLI EQIVVALGGE FKLYLPQLIP HML RVFMHD NSPGRIVSIK LLAAIQLFGA NLDDYLHLLL PPIVKLFDAP EAPLPSRKAA LETVDRLTES LDFTDYASRI IHPI VRTLD QSPELRSTAM DTLSSLVFQL GKKYQIFIPM VNKVLVRHRI NHQRYDVLIC RIVKGYTLAD EEEDPLIYQH RMLRS GQGD ALASGPVETG PMKKLHVSTI NLQKAWGAAR RVSKDDWLEW LRRLSLELLK DSSSPSLRSC WALAQAYNPM ARDLFN AAF VSCWSELNED QQDELIRSIE LALTSQDIAE VTQTLLNLAE FMEHSDKGPL PLRDDNGIVL LGERAAKCRA YAKALHY KE LEFQKGPTPA ILESLISINN KLQQPEAAAG VLEYAMKHFG ELEIQATWYE KLHEWEDALV AYDKKMDTNK DDPELMLG R MRCLEALGEW GQLHQQCCEK WTLVNDETQA KMARMAAAAA WGLGQWDSME EYTCMIPRDT HDGAFYRAVL ALHQDLFSL AQQCIDKARD LLDAELTAMA GESYSRAYGA MVSCHMLSEL EEVIQYKLVP ERREIIRQIW WERLQGCQRI VEDWQKILMV RSLVVSPHE DMRTWLKYAS LCGKSGRLAL AHKTLVLLLG VDPSRQLDHP LPTVHPQVTY AYMKNMWKSA RKIDAFQHMQ H FVQTMQQQ AQHAIATEDQ QHKQELHKLM ARCFLKLGEW QLNLQGINES TIPKVLQYYS AATEHDRSWY KAWHAWAVMN FE AVLHYKH QNQARDEKKK LRHASGANIT NATTAATTAA TATTTASTEG SNSESEAEST ENSPTPSPLQ KKVTEDLSKT LLM YTVPAV QGFFRSISLS RGNNLQDTLR VLTLWFDYGH WPDVNEALVE GVKAIQIDTW LQVIPQLIAR IDTPRPLVGR LIHQ LLTDI GRYHPQALIY PLTVASKSTT TARHNAANKI LKNMCEHSNT LVQQAMMVSE ELIRVAILWH EMWHEGLEEA SRLYF GERN VKGMFEVLEP LHAMMERGPQ TLKETSFNQA YGRDLMEAQE WCRKYMKSGN VKDLTQAWDL YYHVFRRISK QLPQLT SLE LQYVSPKLLM CRDLELAVPG TYDPNQPIIR IQSIAPSLQV ITSKQRPRKL TLMGSNGHEF VFLLKGHEDL RQDERVM QL FGLVNTLLAN DPTSLRKNLS IQRYAVIPLS TNSGLIGWVP HCDTLHALIR DYREKKKILL NIEHRIMLRM APDYDHLT L MQKVEVFEHA VNNTAGDDLA KLLWLKSPSS EVWFDRRTNY TRSLAVMSMV GYILGLGDRH PSNLMLDRLS GKILHIDFG DCFEVAMTRE KFPEKIPFRL TRMLTNAMEV TGLDGNYRIT CHTVMEVLRE HKDSVMAVLE AFVYDPLLNW RLMDTNTKGN KRSRTRTDS YSAGQSVEIL DGVELGEPAH KKTGTTVPES IHSFIGDGLV KPEALNKKAI QIINRVRDKL TGRDFSHDDT L DVPTQVEL LIKQATSHEN LCQCYIGWCP FW

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: 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: 195.552031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDHDGD YKDHDIDYKD DDDKGTMAAI GRGRSLKNLR VRGRNDSGEE NVPLDLTREP SDNLREILQN VARLQGVSNM RKLGHLNNF TKLLCDIGHS EEKLGFHYED IIICLRLALL NEAKEVRAAG LRALRYLIQD SSILQKVLKL KVDYLIARCI D IQQSNEVE ...String:
MADYKDHDGD YKDHDIDYKD DDDKGTMAAI GRGRSLKNLR VRGRNDSGEE NVPLDLTREP SDNLREILQN VARLQGVSNM RKLGHLNNF TKLLCDIGHS EEKLGFHYED IIICLRLALL NEAKEVRAAG LRALRYLIQD SSILQKVLKL KVDYLIARCI D IQQSNEVE RTQALRLVRK MITVNASLFP SSVTNSLIAV GNDGLQERDR MVRACIAIIC ELALQNPEVV ALRGGLNTIL KN VIDCQLS RINEALITTI LHLLNHPKTR QYVRADVELE RILAPYTDFH YRHSPDTAEG QLKEDREARF LASKMGIIAT FRS WAGIIN LCKPGNSGIQ SLIGVLCIPN MEIRRGLLEV LYDIFRLPLP VVTEEFIEAL LSVDPGRFQD SWRLSDGFVA AEAK TILPH RARSRPDLMD NYLALILSAF IRNGLLEGLV EVITNSDDHI SVRATILLGE LLHMANTILP HSHSHHLHCL PTLMN MAAS FDIPKEKRLR ASAALNCLKR FHEMKKRGPK PYSLHLDHII QKAIATHQKR DQYLRVQKDI FILKDTEEAL LINLRD SQV LQHKENLEWN WNLIGTILKW PNVNLRNYKD EQLHRFVRRL LYFYKPSSKL YANLDLDFAK AKQLTVVGCQ FTEFLLE SE EDGQGYLEDL VKDIVQWLNA SSGMKPERSL QNNGLLTTLS QHYFLFIGTL SCHPHGVKML EKCSVFQCLL NLCSLKNQ D HLLKLTVSSL DYSRDGLARV ILSKILTAAT DACRLYATKH LRVLLRANVE FFNNWGIELL VTQLHDKNKT ISSEALDIL DEACEDKANL HALIQMKPAL SHLGDKGLLL LLRFLSIPKG FSYLNERGYV AKQLEKWHRE YNSKYVDLIE EQLNEALTTY RKPVDGDNY VRRSNQRLQR PHVYLPIHLY GQLVHHKTGC HLLEVQNIIT ELCRNVRTPD LDKWEEIKKL KASLWALGNI G SSNWGLNL LQEENVIPDI LKLAKQCEVL SIRGTCVYVL GLIAKTKQGC DILKCHNWDA VRHSRKHLWP VVPDDVEQLC NE LSSIPST LSLNSESTSS RHNSESESVP SSMFILEDDR FGSSSTSTFF LDINEDTEPT FYDRSGPIKD KNSFPFFASS KLV KNRILN SLTLPNKKHR SSSDPKGGKL SSESKTSNRR IRTLTEPSVD FNHSDDFTPI STVQKTLQLE TSFMGNKHIE DTGS TPSIG ENDLKFTKNF GTENHRENTS RERLVVESST SSHMKIRSQS FNTDTTTSGI SSMSSSPSRE TVGVDATTMD TDCGS MSTV VSTKTIKTSH YLTPQSNHLS LSKSNSVSLV PPGSSHTLPR RAQSLKAPSI ATIKSLADCN FSYTSSRDAF GYATLK RLQ QQRMHPSLSH SEALASPAKD VLFTDTITMK ANSFESRLTP SRFMKALSYA SLDKEDLLSP INQNTLQRSS SVRSMVS SA TYGGSDDYIG LALPVDINDI FQVKDIPYFQ TKNIPPHDDR GARAFAHDAG GLPSGTGGLV KNSFHLLRQQ MSLTEIMN S IHSDASLFLE STEDTGLQEH TDDNCLYCVC IEILGFQPSN QLSAICSHSD FQDIPYSDWC EQTIHNPLEV VPSKFSGIS GCSDGVSQEG SASSTKSTEL LLGVKTIPDD TPMCRILLRK EVLRLVINLS SSVSTKCHET GLLTIKEKYP QTFDDICLYS EVSHLLSHC TFRLPCRRFI QELFQDVQFL QMHEEAEAVL ATPPKQPIVD TSAES

UniProtKB: Rapamycin-insensitive companion of mTOR

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Macromolecule #4: Target of rapamycin complex 2 subunit MAPKAP1

MacromoleculeName: Target of rapamycin complex 2 subunit MAPKAP1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.101582 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (ACE)AFLDNPTII LAHIRQSHVT SDDTGMCEMV LIDHDVDLEK IHPPSMPGDS GSEIQGSNGE TQGYVYAQSV DITSSW DFG IRRRSNTAQR LERLRKERQN QIKCKNIQWK ERNSKQSAQE LKSLFEKKSL KEKPPISGKQ SILSVRLEQC PLQLNNP FN EYSKFDGKGH ...String:
(ACE)AFLDNPTII LAHIRQSHVT SDDTGMCEMV LIDHDVDLEK IHPPSMPGDS GSEIQGSNGE TQGYVYAQSV DITSSW DFG IRRRSNTAQR LERLRKERQN QIKCKNIQWK ERNSKQSAQE LKSLFEKKSL KEKPPISGKQ SILSVRLEQC PLQLNNP FN EYSKFDGKGH VGTTATKKID VYLPLHSSQD RLLPMTVVTM ASARVQDLIG LICWQYTSEG REPKLNDNVS AYCLHIAE D DGEVDTDFPP LDSNEPIHKF GFSTLALVEK YSSPGLTSKE SLFVRINAAH GFSLIQVDNT KVTMKEILLK AVKRRKGSQ KVSGPQYRLE KQSEPNVAVD LDSTLESQSA WEFCLVRENS SRADGVFEED SQIDIATVQD MLSSHHYKSF KVSMIHRLRF TTDVQLGIS GDKVEIDPVT NQKASTKFWI KQKPISIDSD LLCACDLAEE KSPSHAIFKL TYLSNHDYKH LYFESDAATV N EIVLKVNY ILESRASTAR ADYFAQKQRK LNRRTSFSFQ KEKKSGQQ

UniProtKB: Target of rapamycin complex 2 subunit MAPKAP1

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Macromolecule #5: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 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

Concentration0.9 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMHEPES
250.0 mMNaCl
1.0 mMTCEP
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 287 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: De novo initial 3D model generation in RELION 5.0
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 191304
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4 / Avg.num./class: 200000

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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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