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- EMDB-80083: Cryo-EM map of the human KICSTOR complex (full length) -

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Basic information

Entry
Database: EMDB / ID: EMD-80083
TitleCryo-EM map of the human KICSTOR complex (full length)
Map data
Sample
  • Complex: The human KPTN-ITFG2-C12orf66-SZT2 complex
    • Protein or peptide: KICSTOR complex protein kaptin
    • Protein or peptide: KICSTOR complex protein ITFG2
    • Protein or peptide: KICSTOR complex protein C12orf66
    • Protein or peptide: KICSTOR complex protein SZT2
KeywordsComplex / lysosome / mTORC1 / SIGNALING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsYang A / Liang L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32571452 China
CitationJournal: To Be Published
Title: Mechanistic insights into GATOR1 inhibition by GATOR2 and KICSTOR
Authors: Yang A / Liang L
History
DepositionApr 1, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80083.png

Downloads & links

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Map

FileDownload / File: emd_80083.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 400 pix.
= 465.408 Å		1.16 Å/pix.
x 400 pix.
= 465.408 Å		1.16 Å/pix.
x 400 pix.
= 465.408 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16352 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.235481 - 2.240181
Average (Standard dev.)0.000474998 (±0.029657988)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 465.408 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_80083_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_80083_half_map_2.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 : The human KPTN-ITFG2-C12orf66-SZT2 complex

EntireName: The human KPTN-ITFG2-C12orf66-SZT2 complex
Components
  • Complex: The human KPTN-ITFG2-C12orf66-SZT2 complex
    • Protein or peptide: KICSTOR complex protein kaptin
    • Protein or peptide: KICSTOR complex protein ITFG2
    • Protein or peptide: KICSTOR complex protein C12orf66
    • Protein or peptide: KICSTOR complex protein SZT2

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Supramolecule #1: The human KPTN-ITFG2-C12orf66-SZT2 complex

SupramoleculeName: The human KPTN-ITFG2-C12orf66-SZT2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: KICSTOR complex protein kaptin

MacromoleculeName: KICSTOR complex protein kaptin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: GMMGEAAVAA GPCPLREDSF TRFSSQSNVY GLAGGAGGRG ELLAATLKGK VLGFRYQDLR Q KIRPVAKE LQFNYIPVDA EIVSIDTFNK SPPKRGLVVG ITFIKDSGDK GSPFLNIYCD YE PGSEYNL DSIAQSCLNL ELQFTPFQLC HAEVQVGDQL ETVFLLSGND ...String:
GMMGEAAVAA GPCPLREDSF TRFSSQSNVY GLAGGAGGRG ELLAATLKGK VLGFRYQDLR Q KIRPVAKE LQFNYIPVDA EIVSIDTFNK SPPKRGLVVG ITFIKDSGDK GSPFLNIYCD YE PGSEYNL DSIAQSCLNL ELQFTPFQLC HAEVQVGDQL ETVFLLSGND PAIHLYKENE GLH QFEEQP VENLFPELTN LTSSVLWLDV HNFPGTSRRL SALGCQSGYV RVAHVDQRSR EVLQ MWSVL QDGPISRVIV FSLSAAKETK DRPLQDEYSV LVASMLEPAV VYRDLLNRGL EDQLL LPGS DQFDSVLCSL VTDVDLDGRP EVLVATYGQE LLCYKYRGPE SGLPEAQHGF HLLWQR SFS SPLLAMAHVD LTGDGLQELA VVSLKGVHIL QHSLIQASEL VLTRLRHQVE QRRRRLQ GL EDGAGAGPAE NAAS

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Macromolecule #2: KICSTOR complex protein ITFG2

MacromoleculeName: KICSTOR complex protein ITFG2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MRSVSYVQRV ALEFSGSLFP HAICLGDVDN DTLNELVVGD TSGKVSVYKN DDSRPWLTCS CQGMLTCVG VGDVCNKGKN LLVAVSAEGW FHLFDLTPAK VLDASGHHET LIGEEQRPVF K QHIPANTK VMLISDIDGD GCRELVVGYT DRVVRAFRWE ELGEGPEHLT ...String:
MRSVSYVQRV ALEFSGSLFP HAICLGDVDN DTLNELVVGD TSGKVSVYKN DDSRPWLTCS CQGMLTCVG VGDVCNKGKN LLVAVSAEGW FHLFDLTPAK VLDASGHHET LIGEEQRPVF K QHIPANTK VMLISDIDGD GCRELVVGYT DRVVRAFRWE ELGEGPEHLT GQLVSLKKWM LE GQVDSLS VTLGPLGLPE LMVSQPGCAY AILLCTWKKD TGSPPASEGP TDGSRETPAA RDV VLHQTS GRIHNKNVST HLIGNIKQGH GTESSGSGLF ALCTLDGTLK LMEEMEEADK LLWS VQVDH QLFALEKLDV TGNGHEEVVA CAWDGQTYII DHNRTVVRFQ VDENIRAFCA GLYAC KEGR NSPCLVYVTF NQKIYVYWEV QLERMESTNL VKLLETKPEY HSLLQELGVD PDDLPV TRA LLHQTLYHPD QPPQCAPSSL QDPT

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Macromolecule #3: KICSTOR complex protein C12orf66

MacromoleculeName: KICSTOR complex protein C12orf66 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MGESIPLAAP VPVEQAVLET FFSHLGIFSY DKAKDNVEKE REANKSAGGS WLSLLAALAH LAAAEKVYH SLTYLGQKLG GQSFFSRKDS IRTIYTSLHN ELKKVVTGRG ALGGTAPHVE E LLSHLSEQ LCFFVQARME IADFYEKMYT LSTQKFINAE ELVGLLDAIM ...String:
MGESIPLAAP VPVEQAVLET FFSHLGIFSY DKAKDNVEKE REANKSAGGS WLSLLAALAH LAAAEKVYH SLTYLGQKLG GQSFFSRKDS IRTIYTSLHN ELKKVVTGRG ALGGTAPHVE E LLSHLSEQ LCFFVQARME IADFYEKMYT LSTQKFINAE ELVGLLDAIM KKYSSRFHHP IL SPLESSF QLEVDVLCHL LKAQAQVSEW KFLPSLVNLH SAHTKLQTWG QIFEKQRETK KHL FGGQSQ KAVQPPHLFL WLMKLKNMLL AKFSFYFHEA LSRQTTASEM KTLTAKANPD FFGK ISSFI RKYDAANVSL IFDNRGSESF QGHGYHHPHS YREAPKGVDQ YPAVVSLPSD RPVMH WPNV IMIMTDRTSD LNSLEKVVHF YDDKVQSTYF LTRPEPHFTI VIIFESKKSE RDSHFI SFL NEVSLALKNP KVFASLKPGA KG

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Macromolecule #4: KICSTOR complex protein SZT2

MacromoleculeName: KICSTOR complex protein SZT2 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: GMASERPEPE VEEAGQVFLL MKKDYRISRN VRLAWFLSHL HQTVQATPQE MLLQSEQELE V LSVLPPGW QPDEPVVPRP FLLVPSTRVT FLAWQYRFVI ELDLSPSTGI VDDSTGEILF DE VFHALSR CLGGLLRPFR VPGSCIDFQP EIYVTIQAYS SIIGLQSHQV ...String:
GMASERPEPE VEEAGQVFLL MKKDYRISRN VRLAWFLSHL HQTVQATPQE MLLQSEQELE V LSVLPPGW QPDEPVVPRP FLLVPSTRVT FLAWQYRFVI ELDLSPSTGI VDDSTGEILF DE VFHALSR CLGGLLRPFR VPGSCIDFQP EIYVTIQAYS SIIGLQSHQV LVQGCLLDPS QRE VFLQQI YEQLCLFEDK VATMLQQQYD PQSQAEDQSP DSGDLLGRKV GVSMVTADLG LVSM IRQGI LALQLLPSNS SAGIIVITDG VTSVPDVAVC ETLLNQLRSG TVACSFVQVG GVYSY DCSF GHVPNVELMK FIAMATFGSY LSTCPEPEPG NLGLTVYHRA FLLYSFLRSG EALNPE YYC GSQHRLFNEH LVSASSNPAL ALRRKKHTEK EVPADLVSTV SVRLREGYSV REVTLAK GG SQLEVKLVLL WKHNMRIEYV AMAPWPLEPE GPRVTRVEVT MEGGYDILHD VSCALRQP I RSLYRTHVIR RFWNTLQSIN QTDQMLAHLQ SFSSVPEHFT LPDSTKSGVP LFYIPPGST TPVLSLQPSG SDSSHAQFAA YWKPVLSMDA NSWQRWLHMH RLVLILEHDT PIPKHLHTPG SNGRYSTIQ CRISHSSLTS LLRDWSSFVL VEGYSYVKLL SSAPDQPPNS FYMVRIISKA P CMVLRLGF PIGTPAPARH KIVSGLREEI LRLRFPHRVQ SKEPTPKVKR KGLGGAGGGS SP SKSPPVL GPQQALSDRP CLVVLHKPLD KLLIRYEKLP LDYRAPFLLT LEPPGPLPLV SGR SASSSL ASLSRYLYHQ RWLWSVPSGL APALPLSAIA QLLSILTEVR LSEGFHFACS GEGI INMVL ELPIQNEPPG QAAAEEKHTC VVQYILFPPH STSTKDSFST DDDNDVEVEA LEGDS ELNL VTEVWVEPQY GRVGPGPGIW KHLQDLTYSE IPQALHPRDA ACIGSMLSFE YLIQLC QSK EWGPLPPEPR VSDGLDQGGD TCVHEIPFHF DLMGLLPQCQ QLQMFFLLLA REPEGVP FA EGSCPANDMV LCLLHSCLGQ ELSDREIPLT PVDQAAFLSE VLRRTCHVPG AEGPLLGV H GIPKEQAVGS TQATGDSAFT SLSVGLPETL KPLISAQPPQ WRCYARLVNP QHVFLTFLP ATFSDVQRLA ACGLEGPPQE ETKPKFGDWS GAPSLKDLGG TGIKATKSHV PVLSVTLASD NAQNQGELS PPFRRDLQAY AGRQASQTES ADGPRTRCPV YIYSCSLEAL REQMVGMQPP Q APRDLIFR TQFLDHPSPS SAWMEPRYKE AANHCALLQE HAQRCYVRGL FRSLQQAQSV TS QDLLTAV DACEELLQEI DITPFLLALC GHTWGLPHAP PSPGPLSPGP FSSSMEEGAE PRE RAILAS ESSIETEDLS EPEFQSTRVP GIPDPGPEIS LTDVCQLRGE AHGALHSVIQ EKFL EISRL HFRTVPSNPH YFFYCPPSSR REDEGPRDTV DRKISDLEFS EAELMGEEGD TSACC VVTE SDPELEVEYR ESRESDLGPA GLDSASLSDV DTVNPDEDSF SILGGDSPTG PESFLH DLP PLFLHLTCSV RLRGQHSSVP VCSLPTCLGQ VLSSLEGPPV GGRVPLRDLS VTLDVFM LT LPLEVELPTA SDPQHHRSTS ESSASFPRSP GQPSSLRSDD GLGPPLPPPE EERHPGLS N LATPHRLAIE TTMNEIRWLL EDEMVGALRR GGIPQSPALH RAAAHIHSSP GRSTCLRQT LPLSFVFGPE RSLTQFKEEF RRLHLPGHVL LEDPDSGFFF VAAGQQPGGS HGEPSSAAWA WHSHEDRAE GIEGETLTAS PQAPGSPEDS EGVPLISLPR VPQGGSQPGP SRGLSLMSSQ G SVDSDHLG YDGGSSGSDS EGPNDTLGEK APFTLRTPPG PAPPQPSLSG LPGPCLPDFW LI VRVLQDR VEVYAHARSL IREDGGPGTE CRHLQQLLVR RVGEICREVN QRLLLQDLHD SHV CNSLLV AESEEDLWRS ETPFHSRQRA PLPSDDYAAD ESCAPRGYLA ATMQFVPGHF SCDV VWGTV IRVHSRLKMG PSMGVSRAIQ ALRSVLNAFS VVNRKNMFVY QERATKAVYY LRLLE TSCS DRPWKGDALP PSLALSRSQE PIYSEEASGP RSPLDMVSSR SSDAARPVGQ VDRHIQ LLV HGVGQAGPEI TDELVRVLCR RLDEATLDVI TVMLVRNCKL TPADVEFIQP PGSLPSE VL HLALPTSCRP WLPALAWYLR QNLLIFLHSP KYTDSNSRNH FQHPLPPQGG LPDLDIYL Y NKPGGQGTGG KGVACITLAF VDEGGAPLSL ALWPPSSPGP PDPLREEEFE QLTQVIRCP VVVDSSSAQN GAPRLRLDVW EKGNISIVQL EEKLRGAARQ ALADAIIELQ LLPASLCTED TPTGSLRNG SLETKSSAGR ASTFPPAPVP GEPVTPPSKA GRRSFWDMLS KTECGDLGSP K TTDDIVLD RPEDTRGRRR HKTESVRTPG GAERAPGSDS GAQRQKRRTT QLEEGEVGTL HP VFARVAQ RWMEFMVQIG CASVSRSSAH MVSRFLLPSI LSEFTALVTS MAGDTSVRIF EQH LGSEPE IFGPCSPGQL GPSPRPAAER HLLLLGRNFL QWRRPTQQAA KAMQRFEPGG DGSS GRNAP RQRLLLLEVV DKKLQLLTYN WAPDLGAALG RALVRLVQWQ NARAHLIFCL LSQKL GLFH HYGQLDFPVR DEKEPNPFLL PTMEVETLIR SASPPLSREQ GRLSGSSRGG GPLPLD TFP FDEALRDITA ARPSSVLGPV PRPPDPVTYH GQQFLEIKMA ERRELERQMK MENLFVT WQ QRSTPATMPI SAGELETLKQ SSRLVHYCAT AMLFDPAAWL HGPPETSGPP DGQRRHRP E SGSGSREAPT SCESLDVSPP GAREEPWLKE LSLAFLQQYV QYLQSIGFVL VPLRPPSPA RSTSRPRAMA ILGTEGRGSF SCPKTKTDGS PKSTSSPVTT YHLQRALPGG IILMELAFQG CYFCVKQFA LECSRIPMGQ AVNSQLSMLF TEECDKVRDL MHVHSFSYDF HLRLVHQHVL G AHLVLRHG YHLTTFLRHF LAHHPDGPHF GRNHIYQGTL ELPTPLIAAH QLYNYVADHA SS YHMKPLR MARPGGPEHN EYALVSAWHS SGSYLDSEGL RHQDDFDVSL LVCHCAAPFE EQG EAERHV LRLQFFVVLT SQRELFPRLT ADMRRFRKPP RLPPEPEAPG SSAGSPGEAS GLIL APGPA PLFPPLAAEV GMARARLAQL VRLAGGHCRR DTLWKRLFLL EPPGPDRLRL GGRLA LAEL EELLEAVHAK SIGDIDPQLD CFLSMTVSWY QSLIKVLLSR FPQSCRHFQS PDLGTQ YLV VLNQKFTDCF VLVFLDSHLG KTSLTVVFRE PFPVQPQDSE SPPAQLVSTY HHLESVI NT ACFTLWTRLL

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (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 / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 39012
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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