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- EMDB-26213: the apo structure of human mTORC2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-26213
Titlethe apo structure of human mTORC2 complex
Map data
Sample
  • Complex: apostate of mTORC2 complex, composed of mTOR, Rictor, mLST8 and mSin1
    • 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
Keywordscomplex / SIGNALING PROTEIN
Function / homology
Function and homology information


TORC2 signaling / regulation of peptidyl-serine phosphorylation / positive regulation of cytoplasmic translational initiation / positive regulation of pentose-phosphate shunt / RNA polymerase III type 1 promoter sequence-specific DNA binding / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation ...TORC2 signaling / regulation of peptidyl-serine phosphorylation / positive regulation of cytoplasmic translational initiation / positive regulation of pentose-phosphate shunt / RNA polymerase III type 1 promoter sequence-specific DNA binding / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / regulation of membrane permeability / TFIIIC-class transcription factor complex binding / heart valve morphogenesis / negative regulation of lysosome organization / RNA polymerase III type 3 promoter sequence-specific DNA binding / TORC2 complex / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / regulation of cellular response to oxidative stress / regulation of autophagosome assembly / calcineurin-NFAT signaling cascade / nucleus localization / TORC1 signaling / 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 / phosphatidic acid binding / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of cell size / ruffle organization / phosphatidylinositol-3,4-bisphosphate binding / negative regulation of Ras protein signal transduction / cellular response to osmotic stress / negative regulation of protein localization to nucleus / anoikis / cardiac muscle cell development / phosphatidylinositol-3,5-bisphosphate binding / regulation of establishment of cell polarity / embryo development ending in birth or egg hatching / positive regulation of transcription by RNA polymerase III / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / regulation of cell size / Macroautophagy / positive regulation of oligodendrocyte differentiation / negative regulation of macroautophagy / positive regulation of actin filament polymerization / lysosome organization / positive regulation of myotube differentiation / behavioral response to pain / oligodendrocyte differentiation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Constitutive Signaling by AKT1 E17K in Cancer / mTORC1-mediated signalling / germ cell development / CD28 dependent PI3K/Akt signaling / cellular response to nutrient levels / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of phosphoprotein phosphatase activity / HSF1-dependent transactivation / positive regulation of TOR signaling / TOR signaling / neuronal action potential / positive regulation of translational initiation / response to amino acid / regulation of macroautophagy / endomembrane system / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of lamellipodium assembly / positive regulation of epithelial to mesenchymal transition / positive regulation of lipid biosynthetic process / heart morphogenesis / cardiac muscle contraction / regulation of cellular response to heat / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / cytoskeleton organization / T cell costimulation / substantia nigra development / phosphatidylinositol-4,5-bisphosphate binding / cellular response to amino acid starvation / phagocytic vesicle / positive regulation of glycolytic process / cellular response to starvation / negative regulation of autophagy / protein serine/threonine kinase activator activity / response to nutrient levels / response to nutrient / post-embryonic development / VEGFR2 mediated vascular permeability / regulation of signal transduction by p53 class mediator / Regulation of PTEN gene transcription / positive regulation of translation / regulation of cell growth / regulation of actin cytoskeleton organization
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 / 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 / PIK-related kinase, FAT / FAT domain / FATC domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Quinoprotein alcohol dehydrogenase-like superfamily / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / 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. / WD domain, G-beta repeat / 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: 3.28 Å
AuthorsYu Z / Chen J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J Biol Chem / Year: 2022
Title: Interactions between mTORC2 core subunits Rictor and mSin1 dictate selective and context-dependent phosphorylation of substrate kinases SGK1 and Akt.
Authors: Zanlin Yu / Junliang Chen / Enzo Takagi / Feng Wang / Bidisha Saha / Xi Liu / Lydia-Marie Joubert / Catherine E Gleason / Mingliang Jin / Chengmin Li / Carlos Nowotny / David Agard / Yifan ...Authors: Zanlin Yu / Junliang Chen / Enzo Takagi / Feng Wang / Bidisha Saha / Xi Liu / Lydia-Marie Joubert / Catherine E Gleason / Mingliang Jin / Chengmin Li / Carlos Nowotny / David Agard / Yifan Cheng / David Pearce /
Abstract: Mechanistic target of rapamycin complex 2 (mTORC2) is a multi-subunit kinase complex, central to multiple essential signaling pathways. Two core subunits, Rictor and mSin1, distinguish it from the ...Mechanistic target of rapamycin complex 2 (mTORC2) is a multi-subunit kinase complex, central to multiple essential signaling pathways. Two core subunits, Rictor and mSin1, distinguish it from the related mTORC1 and support context-dependent phosphorylation of its substrates. mTORC2 structures have been determined previously; however, important questions remain, particularly regarding the structural determinants mediating substrate specificity and context-dependent activity. Here, we used cryo-EM to obtain high-resolution structures of the human mTORC2 apo-complex in the presence of substrates Akt and SGK1. Using functional assays, we then tested predictions suggested by substrate-induced structural changes in mTORC2. For the first time, we visualized in the apo-state the side chain interactions between Rictor and mTOR that sterically occlude recruitment of mTORC1 substrates and confer resistance to the mTORC1 inhibitor rapamycin. Also in the apo-state, we observed that mSin1 formed extensive contacts with Rictor via a pair of short α-helices nestled between two Rictor helical repeat clusters, as well as by an extended strand that makes multiple weak contacts with Rictor helical cluster 1. In co-complex structures, we found that SGK1, but not Akt, markedly altered the conformation of the mSin1 N-terminal extended strand, disrupting multiple weak interactions while inducing a large rotation of mSin1 residue Arg-83, which then interacts with a patch of negatively charged residues within Rictor. Finally, we demonstrate mutation of Arg-83 to Ala selectively disrupts mTORC2-dependent phosphorylation of SGK1, but not of Akt, supporting context-dependent substrate selection. These findings provide new structural and functional insights into mTORC2 specificity and context-dependent activity.
History
DepositionFeb 16, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26213.png

Downloads & links

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Map

FileDownload / File: emd_26213.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 2.64
Minimum - Maximum-11.647442 - 22.607026999999999
Average (Standard dev.)0.025841018 (±1.0290349)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 356.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : apostate of mTORC2 complex, composed of mTOR, Rictor, mLST8 and mSin1

EntireName: apostate of mTORC2 complex, composed of mTOR, Rictor, mLST8 and mSin1
Components
  • Complex: apostate of mTORC2 complex, composed of mTOR, Rictor, mLST8 and mSin1
    • 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

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Supramolecule #1: apostate of mTORC2 complex, composed of mTOR, Rictor, mLST8 and mSin1

SupramoleculeName: apostate of mTORC2 complex, composed of mTOR, Rictor, mLST8 and mSin1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serine/threonine-protein kinase mTOR

MacromoleculeName: Serine/threonine-protein kinase mTOR / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 302.330406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVTTLSGLSG EQGPSGDMTT EEDSATHIKF SKRDEDGREL AGATMELRDS SGKTISTWIS DGHVKDFYLY PGKYTFVETA APDGYEVAT PIEFTVNEDG QVTVDGEATE GDAHTGSSGS GSGTGSMLGT GPAAATTAAT TSSNVSVLQQ FASGLKSRNE E TRAKAAKE ...String:
MVTTLSGLSG EQGPSGDMTT EEDSATHIKF SKRDEDGREL AGATMELRDS SGKTISTWIS DGHVKDFYLY PGKYTFVETA APDGYEVAT PIEFTVNEDG QVTVDGEATE GDAHTGSSGS GSGTGSMLGT GPAAATTAAT TSSNVSVLQQ FASGLKSRNE E TRAKAAKE LQHYVTMELR EMSQEESTRF YDQLNHHIFE LVSSSDANER KGGILAIASL IGVEGGNATR IGRFANYLRN LL PSNDPVV MEMASKAIGR LAMAGDTFTA EYVEFEVKRA LEWLGADRNE GRRHAAVLVL RELAISVPTF FFQQVQPFFD NIF VAVWDP KQAIREGAVA ALRACLILTT QREPKEMQKP QWYRHTFEEA EKGFDETLAK EKGMNRDDRI HGALLILNEL VRIS SMEGE RLREEMEEIT QQQLVHDKYC KDLMGFGTKP RHITPFTSFQ AVQPQQSNAL VGLLGYSSHQ GLMGFGTSPS PAKST LVES RCCRDLMEEK FDQVCQWVLK CRNSKNSLIQ MTILNLLPRL AAFRPSAFTD TQYLQDTMNH VLSCVKKEKE RTAAFQ ALG LLSVAVRSEF KVYLPRVLDI IRAALPPKDF AHKRQKAMQV DATVFTCISM LARAMGPGIQ QDIKELLEPM LAVGLSP AL TAVLYDLSRQ IPQLKKDIQD GLLKMLSLVL MHKPLRHPGM PKGLAHQLAS PGLTTLPEAS DVGSITLALR TLGSFEFE G HSLTQFVRHC ADHFLNSEHK EIRMEAARTC SRLLTPSIHL ISGHAHVVSQ TAVQVVADVL SKLLVVGITD PDPDIRYCV LASLDERFDA HLAQAENLQA LFVALNDQVF EIRELAICTV GRLSSMNPAF VMPFLRKMLI QILTELEHSG IGRIKEQSAR MLGHLVSNA PRLIRPYMEP ILKALILKLK DPDPDPNPGV INNVLATIGE LAQVSGLEMR KWVDELFIII MDMLQDSSLL A KRQVALWT LGQLVASTGY VVEPYRKYPT LLEVLLNFLK TEQNQGTRRE AIRVLGLLGA LDPYKHKVNI GMIDQSRDAS AV SLSESKS SQDSSDYSTS EMLVNMGNLP LDEFYPAVSM VALMRIFRDQ SLSHHHTMVV QAITFIFKSL GLKCVQFLPQ VMP TFLNVI RVCDGAIREF LFQQLGMLVS FVKSHIRPYM DEIVTLMREF WVMNTSIQST IILLIEQIVV ALGGEFKLYL PQLI PHMLR VFMHDNSPGR IVSIKLLAAI QLFGANLDDY LHLLLPPIVK LFDAPEAPLP SRKAALETVD RLTESLDFTD YASRI IHPI VRTLDQSPEL RSTAMDTLSS LVFQLGKKYQ IFIPMVNKVL VRHRINHQRY DVLICRIVKG YTLADEEEDP LIYQHR MLR SGQGDALASG PVETGPMKKL HVSTINLQKA WGAARRVSKD DWLEWLRRLS LELLKDSSSP SLRSCWALAQ AYNPMAR DL FNAAFVSCWS ELNEDQQDEL IRSIELALTS QDIAEVTQTL LNLAEFMEHS DKGPLPLRDD NGIVLLGERA AKCRAYAK A LHYKELEFQK GPTPAILESL ISINNKLQQP EAAAGVLEYA MKHFGELEIQ ATWYEKLHEW EDALVAYDKK MDTNKDDPE LMLGRMRCLE ALGEWGQLHQ QCCEKWTLVN DETQAKMARM AAAAAWGLGQ WDSMEEYTCM IPRDTHDGAF YRAVLALHQD LFSLAQQCI DKARDLLDAE LTAMAGESYS RAYGAMVSCH MLSELEEVIQ YKLVPERREI IRQIWWERLQ GCQRIVEDWQ K ILMVRSLV VSPHEDMRTW LKYASLCGKS GRLALAHKTL VLLLGVDPSR QLDHPLPTVH PQVTYAYMKN MWKSARKIDA FQ HMQHFVQ TMQQQAQHAI ATEDQQHKQE LHKLMARCFL KLGEWQLNLQ GINESTIPKV LQYYSAATEH DRSWYKAWHA WAV MNFEAV LHYKHQNQAR DEKKKLRHAS GANITNATTA ATTAATATTT ASTEGSNSES EAESTENSPT PSPLQKKVTE DLSK TLLMY TVPAVQGFFR SISLSRGNNL QDTLRVLTLW FDYGHWPDVN EALVEGVKAI QIDTWLQVIP QLIARIDTPR PLVGR LIHQ LLTDIGRYHP QALIYPLTVA SKSTTTARHN AANKILKNMC EHSNTLVQQA MMVSEELIRV AILWHEMWHE GLEEAS RLY FGERNVKGMF EVLEPLHAMM ERGPQTLKET SFNQAYGRDL MEAQEWCRKY MKSGNVKDLT QAWDLYYHVF RRISKQL PQ LTSLELQYVS PKLLMCRDLE LAVPGTYDPN QPIIRIQSIA PSLQVITSKQ RPRKLTLMGS NGHEFVFLLK GHEDLRQD E RVMQLFGLVN TLLANDPTSL RKNLSIQRYA VIPLSTNSGL IGWVPHCDTL HALIRDYREK KKILLNIEHR IMLRMAPDY DHLTLMQKVE VFEHAVNNTA GDDLAKLLWL KSPSSEVWFD RRTNYTRSLA VMSMVGYILG LGDRHPSNLM LDRLSGKILH IDFGDCFEV AMTREKFPEK IPFRLTRMLT NAMEVTGLDG NYRITCHTVM EVLREHKDSV MAVLEAFVYD PLLNWRLMDT N TKGNKRSR TRTDSYSAGQ SVEILDGVEL GEPAHKKTGT TVPESIHSFI GDGLVKPEAL NKKAIQIINR VRDKLTGRDF SH DDTLDVP TQVELLIKQA TSHENLCQCY IGWCPFW

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: 37.998254 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGYPYDVPDY ADLNGGGGGS TMNTSPGTVG SDPVILATAG YDHTVRFWQA HSGICTRTVQ HQDSQVNALE VTPDRSMIAA AGYQHIRMY DLNSNNPNPI ISYDGVNKNI ASVGFHEDGR WMYTGGEDCT ARIWDLRSRN LQCQRIFQVN APINCVCLHP N QAELIVGD ...String:
MGYPYDVPDY ADLNGGGGGS TMNTSPGTVG SDPVILATAG YDHTVRFWQA HSGICTRTVQ HQDSQVNALE VTPDRSMIAA AGYQHIRMY DLNSNNPNPI ISYDGVNKNI ASVGFHEDGR WMYTGGEDCT ARIWDLRSRN LQCQRIFQVN APINCVCLHP N QAELIVGD QSGAIHIWDL KTDHNEQLIP EPEVSITSAH IDPDASYMAA VNSTGNCYVW NLTGGIGDEV TQLIPKTKIP AH TRYALQC RFSPDSTLLA TCSADQTCKI WRTSNFSLMT ELSIKSGNPG ESSRGWMWGC AFSGDSQYIV TASSDNLARL WCV ETGEIK REYGGHQKAV VCLAFNDSVL G

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: 193.846328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG STMAAIGRGR SLKNLRVRGR NDSGEENVPL DLTREPSDNL REILQNVARL QGVSNMRKLG HLNNFTKLLC DIGHSEEKL GFHYEDIIIC LRLALLNEAK EVRAAGLRAL RYLIQDSSIL QKVLKLKVDY LIARCIDIQQ SNEVERTQAL R LVRKMITV ...String:
MDYKDDDDKG STMAAIGRGR SLKNLRVRGR NDSGEENVPL DLTREPSDNL REILQNVARL QGVSNMRKLG HLNNFTKLLC DIGHSEEKL GFHYEDIIIC LRLALLNEAK EVRAAGLRAL RYLIQDSSIL QKVLKLKVDY LIARCIDIQQ SNEVERTQAL R LVRKMITV NASLFPSSVT NSLIAVGNDG LQERDRMVRA CIAIICELAL QNPEVVALRG GLNTILKNVI DCQLSRINEA LI TTILHLL NHPKTRQYVR ADVELERILA PYTDFHYRHS PDTAEGQLKE DREARFLASK MGIIATFRSW AGIINLCKPG NSG IQSLIG VLCIPNMEIR RGLLEVLYDI FRLPLPVVTE EFIEALLSVD PGRFQDSWRL SDGFVAAEAK TILPHRARSR PDLM DNYLA LILSAFIRNG LLEGLVEVIT NSDDHISVRA TILLGELLHM ANTILPHSHS HHLHCLPTLM NMAASFDIPK EKRLR ASAA LNCLKRFHEM KKRGPKPYSL HLDHIIQKAI ATHQKRDQYL RVQKDIFILK DTEEALLINL RDSQVLQHKE NLEWNW NLI GTILKWPNVN LRNYKDEQLH RFVRRLLYFY KPSSKLYANL DLDFAKAKQL TVVGCQFTEF LLESEEDGQG YLEDLVK DI VQWLNASSGM KPERSLQNNG LLTTLSQHYF LFIGTLSCHP HGVKMLEKCS VFQCLLNLCS LKNQDHLLKL TVSSLDYS R DGLARVILSK ILTAATDACR LYATKHLRVL LRANVEFFNN WGIELLVTQL HDKNKTISSE ALDILDEACE DKANLHALI QMKPALSHLG DKGLLLLLRF LSIPKGFSYL NERGYVAKQL EKWHREYNSK YVDLIEEQLN EALTTYRKPV DGDNYVRRSN QRLQRPHVY LPIHLYGQLV HHKTGCHLLE VQNIITELCR NVRTPDLDKW EEIKKLKASL WALGNIGSSN WGLNLLQEEN V IPDILKLA KQCEVLSIRG TCVYVLGLIA KTKQGCDILK CHNWDAVRHS RKHLWPVVPD DVEQLCNELS SIPSTLSLNS ES TSSRHNS ESESVPSSMF ILEDDRFGSS STSTFFLDIN EDTEPTFYDR SGPIKDKNSF PFFASSKLVK NRILNSLTLP NKK HRSSSD PKGGKLSSES KTSNRRIRTL TEPSVDFNHS DDFTPISTVQ KTLQLETSFM GNKHIEDTGS TPSIGENDLK FTKN FGTEN HRENTSRERL VVESSTSSHM KIRSQSFNTD TTTSGISSMS SSPSRETVGV DATTMDTDCG SMSTVVSTKT IKTSH YLTP QSNHLSLSKS NSVSLVPPGS SHTLPRRAQS LKAPSIATIK SLADCNFSYT SSRDAFGYAT LKRLQQQRMH PSLSHS EAL ASPAKDVLFT DTITMKANSF ESRLTPSRFM KALSYASLDK EDLLSPINQN TLQRSSSVRS MVSSATYGGS DDYIGLA LP VDINDIFQVK DIPYFQTKNI PPHDDRGARA FAHDAGGLPS GTGGLVKNSF HLLRQQMSLT EIMNSIHSDA SLFLESTE D TGLQEHTDDN CLYCVCIEIL GFQPSNQLSA ICSHSDFQDI PYSDWCEQTI HNPLEVVPSK FSGISGCSDG VSQEGSASS TKSTELLLGV KTIPDDTPMC RILLRKEVLR LVINLSSSVS TKCHETGLLT IKEKYPQTFD DICLYSEVSH LLSHCTFRLP CRRFIQELF QDVQFLQMHE EAEAVLATPP KQPIVDTSAE S

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: 60.732328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 KEKKSGQQAA AGGGGYPYDV PDYA

UniProtKB: Target of rapamycin complex 2 subunit MAPKAP1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
GridModel: Homemade / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 22 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 288538
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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  • 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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