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- EMDB-11489: cryo-EM structure of human mTOR complex 2 in absence of ATP-gamma-S -

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Basic information

Entry
Database: EMDB / ID: EMD-11489
Titlecryo-EM structure of human mTOR complex 2 in absence of ATP-gamma-S
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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsScaiola A / Mangia F / Imseng S / Boehringer D / Ban N / Maier T
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation179323 Switzerland
Swiss National Science Foundation138262 Switzerland
Swiss National Science Foundation177084 Switzerland
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-
UpdateNov 18, 2020-
Current statusNov 18, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.37
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.37
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11489.png

Downloads & links

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Map

FileDownload / File: emd_11489.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.)
1.35 Å/pix.
x 320 pix.
= 431.6 Å		1.35 Å/pix.
x 320 pix.
= 431.6 Å		1.35 Å/pix.
x 320 pix.
= 431.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34875 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.37 / Movie #1: 0.37
Minimum - Maximum-0.6633469 - 2.030117
Average (Standard dev.)0.0012159084 (±0.076771624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 431.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.348751.348751.34875
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z431.600431.600431.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.6632.0300.001

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Supplemental data

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Mask #1

Fileemd_11489_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11489_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11489_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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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

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Supramolecule #1: human mTOR complex 2

SupramoleculeName: human mTOR complex 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 1.15 MDa

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Macromolecule #1: Serine/threonine-protein kinase mTOR

MacromoleculeName: Serine/threonine-protein kinase mTOR / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MLGTGPAAAT TAATTSSNVS VLQQFASGLK SRNEETRAKA AKELQHYVTM ELREMSQEES TRFYDQLNH HIFELVSSSD ANERKGGILA IASLIGVEGG NATRIGRFAN YLRNLLPSND P VVMEMASK AIGRLAMAGD TFTAEYVEFE VKRALEWLGA DRNEGRRHAA ...String:
MLGTGPAAAT TAATTSSNVS VLQQFASGLK SRNEETRAKA AKELQHYVTM ELREMSQEES TRFYDQLNH HIFELVSSSD ANERKGGILA IASLIGVEGG NATRIGRFAN YLRNLLPSND P VVMEMASK AIGRLAMAGD TFTAEYVEFE VKRALEWLGA DRNEGRRHAA VLVLRELAIS VP TFFFQQV QPFFDNIFVA VWDPKQAIRE GAVAALRACL ILTTQREPKE MQKPQWYRHT FEE AEKGFD ETLAKEKGMN RDDRIHGALL ILNELVRISS MEGERLREEM EEITQQQLVH DKYC KDLMG FGTKPRHITP FTSFQAVQPQ QSNALVGLLG YSSHQGLMGF GTSPSPAKST LVESR CCRD LMEEKFDQVC QWVLKCRNSK NSLIQMTILN LLPRLAAFRP SAFTDTQYLQ DTMNHV LSC VKKEKERTAA FQALGLLSVA VRSEFKVYLP RVLDIIRAAL PPKDFAHKRQ KAMQVDA TV FTCISMLARA MGPGIQQDIK ELLEPMLAVG LSPALTAVLY DLSRQIPQLK KDIQDGLL K MLSLVLMHKP LRHPGMPKGL AHQLASPGLT TLPEASDVGS ITLALRTLGS FEFEGHSLT QFVRHCADHF LNSEHKEIRM EAARTCSRLL TPSIHLISGH AHVVSQTAVQ VVADVLSKLL VVGITDPDP DIRYCVLASL DERFDAHLAQ AENLQALFVA LNDQVFEIRE LAICTVGRLS S MNPAFVMP FLRKMLIQIL TELEHSGIGR IKEQSARMLG HLVSNAPRLI RPYMEPILKA LI LKLKDPD PDPNPGVINN VLATIGELAQ VSGLEMRKWV DELFIIIMDM LQDSSLLAKR QVA LWTLGQ LVASTGYVVE PYRKYPTLLE VLLNFLKTEQ NQGTRREAIR VLGLLGALDP YKHK VNIGM IDQSRDASAV SLSESKSSQD SSDYSTSEML VNMGNLPLDE FYPAVSMVAL MRIFR DQSL SHHHTMVVQA ITFIFKSLGL KCVQFLPQVM PTFLNVIRVC DGAIREFLFQ QLGMLV SFV KSHIRPYMDE IVTLMREFWV MNTSIQSTII LLIEQIVVAL GGEFKLYLPQ LIPHMLR VF MHDNSPGRIV SIKLLAAIQL FGANLDDYLH LLLPPIVKLF DAPEAPLPSR KAALETVD R LTESLDFTDY ASRIIHPIVR TLDQSPELRS TAMDTLSSLV FQLGKKYQIF IPMVNKVLV RHRINHQRYD VLICRIVKGY TLADEEEDPL IYQHRMLRSG QGDALASGPV ETGPMKKLHV STINLQKAW GAARRVSKDD WLEWLRRLSL ELLKDSSSPS LRSCWALAQA YNPMARDLFN A AFVSCWSE LNEDQQDELI RSIELALTSQ DIAEVTQTLL NLAEFMEHSD KGPLPLRDDN GI VLLGERA AKCRAYAKAL HYKELEFQKG PTPAILESLI SINNKLQQPE AAAGVLEYAM KHF GELEIQ ATWYEKLHEW EDALVAYDKK MDTNKDDPEL MLGRMRCLEA LGEWGQLHQQ CCEK WTLVN DETQAKMARM AAAAAWGLGQ WDSMEEYTCM IPRDTHDGAF YRAVLALHQD LFSLA QQCI DKARDLLDAE LTAMAGESYS RAYGAMVSCH MLSELEEVIQ YKLVPERREI IRQIWW ERL QGCQRIVEDW QKILMVRSLV VSPHEDMRTW LKYASLCGKS GRLALAHKTL VLLLGVD PS RQLDHPLPTV HPQVTYAYMK NMWKSARKID AFQHMQHFVQ TMQQQAQHAI ATEDQQHK Q ELHKLMARCF LKLGEWQLNL QGINESTIPK VLQYYSAATE HDRSWYKAWH AWAVMNFEA VLHYKHQNQA RDEKKKLRHA SGANITNATT AATTAATATT TASTEGSNSE SEAESTENSP TPSPLQKKV TEDLSKTLLM YTVPAVQGFF RSISLSRGNN LQDTLRVLTL WFDYGHWPDV N EALVEGVK AIQIDTWLQV IPQLIARIDT PRPLVGRLIH QLLTDIGRYH PQALIYPLTV AS KSTTTAR HNAANKILKN MCEHSNTLVQ QAMMVSEELI RVAILWHEMW HEGLEEASRL YFG ERNVKG MFEVLEPLHA MMERGPQTLK ETSFNQAYGR DLMEAQEWCR KYMKSGNVKD LTQA WDLYY HVFRRISKQL PQLTSLELQY VSPKLLMCRD LELAVPGTYD PNQPIIRIQS IAPSL QVIT SKQRPRKLTL MGSNGHEFVF LLKGHEDLRQ DERVMQLFGL VNTLLANDPT SLRKNL SIQ RYAVIPLSTN SGLIGWVPHC DTLHALIRDY REKKKILLNI EHRIMLRMAP DYDHLTL MQ KVEVFEHAVN NTAGDDLAKL LWLKSPSSEV WFDRRTNYTR SLAVMSMVGY ILGLGDRH P SNLMLDRLSG KILHIDFGDC FEVAMTREKF PEKIPFRLTR MLTNAMEVTG LDGNYRITC HTVMEVLREH KDSVMAVLEA FVYDPLLNWR LMDTNTKGNK RSRTRTDSYS AGQSVEILDG VELGEPAHK KTGTTVPESI HSFIGDGLVK PEALNKKAIQ IINRVRDKLT GRDFSHDDTL D VPTQVELL IKQATSHENL CQCYIGWCPF W

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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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNTSPGTVGS DPVILATAGY DHTVRFWQAH SGICTRTVQH QDSQVNALEV TPDRSMIAAA GYQHIRMYD LNSNNPNPII SYDGVNKNIA SVGFHEDGRW MYTGGEDCTA RIWDLRSRNL Q CQRIFQVN APINCVCLHP NQAELIVGDQ SGAIHIWDLK TDHNEQLIPE ...String:
MNTSPGTVGS DPVILATAGY DHTVRFWQAH SGICTRTVQH QDSQVNALEV TPDRSMIAAA GYQHIRMYD LNSNNPNPII SYDGVNKNIA SVGFHEDGRW MYTGGEDCTA RIWDLRSRNL Q CQRIFQVN APINCVCLHP NQAELIVGDQ SGAIHIWDLK TDHNEQLIPE PEVSITSAHI DP DASYMAA VNSTGNCYVW NLTGGIGDEV TQLIPKTKIP AHTRYALQCR FSPDSTLLAT CSA DQTCKI WRTSNFSLMT ELSIKSGNPG ESSRGWMWGC AFSGDSQYIV TASSDNLARL WCVE TGEIK REYGGHQKAV VCLAFNDSVL G

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Macromolecule #3: Rapamycin-insensitive companion of mTOR

MacromoleculeName: Rapamycin-insensitive companion of mTOR / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAIGRGRSL KNLRVRGRND SGEENVPLDL TREPSDNLRE ILQNVARLQG VSNMRKLGHL NNFTKLLCD IGHSEEKLGF HYEDIIICLR LALLNEAKEV RAAGLRALRY LIQDSSILQK V LKLKVDYL IARCIDIQQS NEVERTQALR LVRKMITVNA SLFPSSVTNS ...String:
MAAIGRGRSL KNLRVRGRND SGEENVPLDL TREPSDNLRE ILQNVARLQG VSNMRKLGHL NNFTKLLCD IGHSEEKLGF HYEDIIICLR LALLNEAKEV RAAGLRALRY LIQDSSILQK V LKLKVDYL IARCIDIQQS NEVERTQALR LVRKMITVNA SLFPSSVTNS LIAVGNDGLQ ER DRMVRAC IAIICELALQ NPEVVALRGG LNTILKNVID CQLSRINEAL ITTILHLLNH PKT RQYVRA DVELERILAP YTDFHYRHSP DTAEGQLKED REARFLASKM GIIATFRSWA GIIN LCKPG NSGIQSLIGV LCIPNMEIRR GLLEVLYDIF RLPLPVVTEE FIEALLSVDP GRFQD SWRL SDGFVAAEAK TILPHRARSR PDLMDNYLAL ILSAFIRNGL LEGLVEVITN SDDHIS VRA TILLGELLHM ANTILPHSHS HHLHCLPTLM NMAASFDIPK EKRLRASAAL NCLKRFH EM KKRGPKPYSL HLDHIIQKAI ATHQKRDQYL RVQKDIFILK DTEEALLINL RDSQVLQH K ENLEWNWNLI GTILKWPNVN LRNYKDEQLH RFVRRLLYFY KPSSKLYANL DLDFAKAKQ LTVVGCQFTE FLLESEEDGQ GYLEDLVKDI VQWLNASSGM KPERSLQNNG LLTTLSQHYF LFIGTLSCH PHGVKMLEKC SVFQCLLNLC SLKNQDHLLK LTVSSLDYSR DGLARVILSK I LTAATDAC RLYATKHLRV LLRANVEFFN NWGIELLVTQ LHDKNKTISS EALDILDEAC ED KANLHAL IQMKPALSHL GDKGLLLLLR FLSIPKGFSY LNERGYVAKQ LEKWHREYNS KYV DLIEEQ LNEALTTYRK PVDGDNYVRR SNQRLQRPHV YLPIHLYGQL VHHKTGCHLL EVQN IITEL CRNVRTPDLD KWEEIKKLKA SLWALGNIGS SNWGLNLLQE ENVIPDILKL AKQCE VLSI RGTCVYVLGL IAKTKQGCDI LKCHNWDAVR HSRKHLWPVV PDDVEQLCNE LSSIPS TLS LNSESTSSRH NSESESVPSS MFILEDDRFG SSSTSTFFLD INEDTEPTFY DRSGPIK DK NSFPFFASSK LVKNRILNSL TLPNKKHRSS SDPKGGKLSS ESKTSNRRIR TLTEPSVD F NHSDDFTPIS TVQKTLQLET SFMGNKHIED TGSTPSIGEN DLKFTKNFGT ENHRENTSR ERLVVESSTS SHMKIRSQSF NTDTTTSGIS SMSSSPSRET VGVDATTMDT DCGSMSTVVS TKTIKTSHY LTPQSNHLSL SKSNSVSLVP PGSSHTLPRR AQSLKAPSIA TIKSLADCNF S YTSSRDAF GYATLKRLQQ QRMHPSLSHS EALASPAKDV LFTDTITMKA NSFESRLTPS RF MKALSYA SLDKEDLLSP INQNTLQRSS SVRSMVSSAT YGGSDDYIGL ALPVDINDIF QVK DIPYFQ TKNIPPHDDR GARAFAHDAG GLPSGTGGLV KNSFHLLRQQ MSLTEIMNSI HSDA SLFLE STEDTGLQEH TDDNCLYCVC IEILGFQPSN QLSAICSHSD FQDIPYSDWC EQTIH NPLE VVPSKFSGIS GCSDGVSQEG SASSTKSTEL LLGVKTIPDD TPMCRILLRK EVLRLV INL SSSVSTKCHE TGLLTIKEKY PQTFDDICLY SEVSHLLSHC TFRLPCRRFI QELFQDV QF LQMHEEAEAV LATPPKQPIV DTSAES

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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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: (ACE)AFLDNPTII LAHIRQSHVT SDDTGMCEMV LIDHDVDLEK IHPPSMPGDS GSEIQGSNGE TQGYVYAQS VDITSSWDFG IRRRSNTAQR LERLRKERQN QIKCKNIQWK ERNSKQSAQE L KSLFEKKS LKEKPPISGK QSILSVRLEQ CPLQLNNPFN EYSKFDGKGH ...String:
(ACE)AFLDNPTII LAHIRQSHVT SDDTGMCEMV LIDHDVDLEK IHPPSMPGDS GSEIQGSNGE TQGYVYAQS VDITSSWDFG IRRRSNTAQR LERLRKERQN QIKCKNIQWK ERNSKQSAQE L KSLFEKKS LKEKPPISGK QSILSVRLEQ CPLQLNNPFN EYSKFDGKGH VGTTATKKID VY LPLHSSQ DRLLPMTVVT MASARVQDLI GLICWQYTSE GREPKLNDNV SAYCLHIAED DGE VDTDFP PLDSNEPIHK FGFSTLALVE KYSSPGLTSK ESLFVRINAA HGFSLIQVDN TKVT MKEIL LKAVKRRKGS QKVSGPQYRL EKQSEPNVAV DLDSTLESQS AWEFCLVREN SSRAD GVFE EDSQIDIATV QDMLSSHHYK SFKVSMIHRL RFTTDVQLGI SGDKVEIDPV TNQKAS TKF WIKQKPISID SDLLCACDLA EEKSPSHAIF KLTYLSNHDY KHLYFESDAA TVNEIVL KV NYILESRAST ARADYFAQKQ RKLNRRTSFS FQKEKKSGQQ

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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

Concentration0.37 mg/mL
BufferpH: 8.5
GridModel: Quantifoil / 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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (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

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71386
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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