9V0J: GATOR1-KICSTOR complex

Cryo-EM structure of GATOR1-KICSTOR complex. Determined by electron microscopy at 2.97 Å resolution. Released 12 Nov 2025.

Method
Electron microscopy
Resolution
2.97 Å
Organism
Homo sapiens
Chains
4
Atoms
14,747
Mol. weight
667.32 kDa
Released
12 Nov 2025

Explore 9V0J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9V0J contains 95 α-helices and 106 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 24 helices, 19 β-strands

ElementResiduesLengthSheet
β-strand9-1681
β-strand20-2781
α-helix34-4411
α-helix48-503
β-strand55-5951
β-strand62-6651
β-strand69-7241
β-strand80-90111
α-helix95-973
α-helix99-11618
α-helix122-1254
α-helix128-13710
α-helix138-1425
β-strand144-14852
β-strand154-15852
α-helix163-1664
α-helix168-1703
β-strand174-17743
β-strand18414
α-helix186-1883
α-helix193-1964
α-helix197-1993
α-helix206-2138
α-helix217-23014
β-strand233-23643
α-helix237-2393
β-strand24415
β-strand24716
α-helix249-2557
α-helix258-26811
β-strand26917
α-helix2701
α-helix274-2763
α-helix284-2874
α-helix297-3004
β-strand30817
α-helix310-31910
β-strand32316
β-strand32615
β-strand32918
α-helix351-3588
α-helix362-3665
β-strand37818
Chain B: 21 helices, 15 β-strands
ElementResiduesLengthSheet
β-strand9-1571
β-strand21-2661
α-helix66-738
α-helix77-793
β-strand84-8851
β-strand91-9551
β-strand123-13191
α-helix136-16025
α-helix168-1769
α-helix195-1973
α-helix201-2099
α-helix210-2145
β-strand216-22169
β-strand225-23069
α-helix232-2354
α-helix245-2517
β-strand260-262310
α-helix267-2704
α-helix280-2878
α-helix296-3027
α-helix306-31813
β-strand323-325310
β-strand333-336411
α-helix349-3557
α-helix361-3644
α-helix365-3684
β-strand372-373211
α-helix386-3905
α-helix392-3954
β-strand403-405311
β-strand406-412712
α-helix507-5159
β-strand521-525512
α-helix526-5327
α-helix537-54610
β-strand551-557712
Chain C: 38 helices, 57 β-strands
ElementResiduesLengthSheet
β-strand10-11213
β-strand23-24213
β-strand38114
β-strand54114
α-helix631
β-strand68-69213
α-helix71-777
β-strand96115
β-strand99-104616
α-helix111-12111
β-strand124-127415
β-strand131-134416
β-strand137-1461016
β-strand149-151316
β-strand153-156415
β-strand161-166616
β-strand170-176717
α-helix179-1824
β-strand184118
β-strand190118
α-helix191-1933
α-helix194-2007
α-helix201-21010
β-strand215-2261217
α-helix239-2413
β-strand243-245317
β-strand249-2621417
α-helix271-2799
α-helix281-2844
β-strand296-298317
α-helix299-3002
α-helix301-3033
α-helix306-31712
β-strand331-337717
β-strand342-343219
α-helix347-35913
β-strand364-368517
α-helix371-3733
β-strand379-381319
β-strand397-398219
β-strand403-407517
α-helix426-4272
β-strand42814
α-helix429-4302
α-helix459-4646
α-helix744-7485
α-helix7501
β-strand751116
α-helix752-7543
β-strand756-757220
β-strand770121
β-strand773-777520
α-helix792-7943
α-helix797-80812
β-strand812-814320
β-strand852-856520
β-strand859-865720
β-strand870-875620
β-strand877121
α-helix880-8823
β-strand886-893817
β-strand902-908717
α-helix913-9153
α-helix918-9269
β-strand942-950922
α-helix953-9619
α-helix979-99315
α-helix1179-11857
β-strand1194123
β-strand1204123
β-strand1205-1206224
α-helix1209-12179
α-helix1224-123613
β-strand1240-1242324
α-helix1250-12512
β-strand1254-1255225
β-strand1257-1260424
α-helix1287-12904
β-strand1296-1298325
β-strand1351-1357722
β-strand1369-1375722
β-strand1377-1378225
β-strand1382126
β-strand1384-1390722
α-helix1395-141117
β-strand1414-1418522
β-strand1439-1442426
α-helix1469-147810
β-strand1482-1484326
β-strand1501-1504426
β-strand1509-1512426
β-strand1545-1550626
α-helix1568-158013
α-helix1583-15853
α-helix1586-159813
Chain D: 12 helices, 15 β-strands
ElementResiduesLengthSheet
β-strand15-19527
α-helix28-3710
β-strand42-43228
α-helix45-473
α-helix51-533
β-strand59-64627
β-strand79-80228
β-strand86-89427
β-strand93-101929
α-helix104-1063
β-strand109130
β-strand116130
α-helix120-13011
β-strand148-156929
β-strand166-167229
β-strand171129
α-helix176-1783
α-helix179-20224
α-helix237-24610
β-strand257-262629
α-helix272-28413
β-strand287-292629
α-helix310-3189
α-helix319-3213
β-strand324-325229
α-helix340-3445
β-strand348-349227

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
GATOR1 complex protein NPRL2Aprotein380Homo sapiensQ8WTW4 (AlphaFold model)
GATOR1 complex protein NPRL3Bprotein569Homo sapiensQ12980 (AlphaFold model)
GATOR1 complex protein DEPDC5Cprotein1603Homo sapiensO75140 (AlphaFold model)
KICSTOR complex protein SZT2Dprotein3432Homo sapiensQ5T011 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>9V0J_1 GATOR1 complex protein NPRL2 (chains A)
MGSGCRIECIFFSEFHPTLGPKITYQVPEDFISRELFDTVQVYIITKPELQNKLITVTAM
EKKLIGCPVCIEHKKYSRNALLFNLGFVCDAQAKTCALEPIVKKLAGYLTTLELESSFVS
MEESKQKLVPIMTILLEELNASGRCTLPIDESNTIHLKVIEQRPDPPVAQEYDVPVFTKD
KEDFFNSQWDLTTQQILPYIDGFRHIQKISAEADVELNLVRIAIQNLLYYGVVTLVSILQ
YSNVYCPTPKVQDLVDDKSLQEACLSYVTKQGHKRASLRDVFQLYCSLSPGTTVRDLIGR
HPQQLQHVDERKLIQFGLMKNLIRRLQKYPVRVTREEQSHPARLYTGCHSYDEICCKTGM
SYHELDERLENDPNIIICWK
Sequence of entity 2 (B), FASTA
>9V0J_2 GATOR1 complex protein NPRL3 (chains B)
MRDNTSPISVILVSSGSRGNKLLFRYPFQRSQEHPASQTSKPRSRYAASNTGDHADEQDG
DSRFSDVILATILATKSEMCGQKFELKIDNVRFVGHPTLLQHALGQISKTDPSPKREAPT
MILFNVVFALRANADPSVINCLHNLSRRIATVLQHEERRCQYLTREAKLILALQDEVSAM
ADGNEGPQSPFHHILPKCKLARDLKEAYDSLCTSGVVRLHINSWLEVSFCLPHKIHYAAS
SLIPPEAIERSLKAIRPYHALLLLSDEKSLLGELPIDCSPALVRVIKTTSAVKNLQQLAQ
DADLALLQVFQLAAHLVYWGKAIIIYPLCENNVYMLSPNASVCLYSPLAEQFSHQFPSHD
LPSVLAKFSLPVSLSEFRNPLAPAVQETQLIQMVVWMLQRRLLIQLHTYVCLMASPSEEE
PRPREDDVPFTARVGGRSLSTPNALSFGSPTSSDDMTLTSPSMDNSSAELLPSGDSPLNQ
RMTENLLASLSEHERAAILSVPAAQNPEDLRMFARLLHYFRGRHHLEEIMYNENTRRSQL
LMLFDKFRSVLVVTTHEDPVIAVFQALLP
Sequence of entity 3 (C), FASTA
>9V0J_3 GATOR1 complex protein DEPDC5 (chains C)
MRTTKVYKLVIHKKGFGGSDDELVVNPKVFPHIKLGDIVEIAHPNDEYSPLLLQVKSLKE
DLQKETISVDQTVTQVFRLRPYQDVYVNVVDPKDVTLDLVELTFKDQYIGRGDMWRLKKS
LVSTCAYITQKVEFAGIRAQAGELWVKNEKVMCGYISEDTRVVFRSTSAMVYIFIQMSCE
MWDFDIYGDLYFEKAVNGFLADLFTKWKEKNCSHEVTVVLFSRTFYDAKSVDEFPEINRA
SIRQDHKGRFYEDFYKVVVQNERREEWTSLLVTIKKLFIQYPVLVRLEQAEGFPQGDNST
SAQGNYLEAINLSFNVFDKHYINRNFDRTGQMSVVITPGVGVFEVDRLLMILTKQRMIDN
GIGVDLVCMGEQPLHAVPLFKLHNRSAPRDSRLGDDYNIPHWINHSFYTSKSQLFCNSFT
PRIKLAGKKPASEKAKNGRDTSLGSPKESENALPIQVDYDAYDAQVFRLPGPSRAQCLTT
CRSVRERESHSRKSASSCDVSSSPSLPSRTLPTEEVRSQASDDSSLGKSANILMIPHPHL
HQYEVSSSLGYTSTRDVLENMMEPPQRDSSAPGRFHVGSAESMLHVRPGGYTPQRALINP
FAPSRMPMKLTSNRRRWMHTFPVGPSGEAIQIHHQTRQNMAELQGSGQRDPTHSSAELLE
LAYHEAAGRHSNSRQPGDGMSFLNFSGTEELSVGLLSNSGAGMNPRTQNKDSLEDSVSTS
PDPILTLSAPPVVPGFCCTVGVDWKSLTTPACLPLTTDYFPDRQGLQNDYTEGCYDLLPE
ADIDRRDEDGVQMTAQQVFEEFICQRLMQGYQIIVQPKTQKPNPAVPPPLSSSPLYSRGL
VSRNRPEEEDQYWLSMGRTFHKVTLKDKMITVTRYLPKYPYESAQIHYTYSLCPSHSDSE
FVSCWVEFSHERLEEYKWNYLDQYICSAGSEDFSLIESLKFWRTRFLLLPACVTATKRIT
EGEAHCDIYGDRPRADEDEWQLLDGFVRFVEGLNRIRRRHRSDRMMRKGTAMKGLQMTGP
ISTHSLESTAPPVGKKGTSALSALLEMEASQKCLGEQQAAVHGGKSSAQSAESSSVAMTP
TYMDSPRKDGAFFMEFVRSPRTASSAFYPQVSVDQTATPMLDGTSLGICTGQSMDRGNSQ
TFGNSQNIGEQGYSSTNSSDSSSQQLVASSLTSSSTLTEILEAMKHPSTGVQLLSEQKGL
SPYCFISAEVVHWLVNHVEGIQTQAMAIDIMQKMLEEQLITHASGEAWRTFIYGFYFYKI
VTDKEPDRVAMQQPATTWHTAGVDDFASFQRKWFEVAFVAEELVHSEIPAFLLPWLPSRP
ASYASRHSSFSRSFGGRSQAAALLAATVPEQRTVTLDVDVNNRTDRLEWCSCYYHGNFSL
NAAFEIKLHWMAVTAAVLFEMVQGWHRKATSCGFLLVPVLEGPFALPSYLYGDPLRAQLF
IPLNISCLLKEGSEHLFDSFEPETYWDRMHLFQEAIAHRFGFVQDKYSASAFNFPAENKP
QYIHVTGTVFLQLPYSKRKFSGQQRRRRNSTSSTNQNMFCEERVGYNWAYNTMLTKTWRS
SATGDEKFADRLLKDFTDFCINRDNRLVTFWTSCLEKMHASAP
Sequence of entity 4 (D), FASTA
>9V0J_4 KICSTOR complex protein SZT2 (chains D)
MASERPEPEVEEAGQVFLLMKKDYRISRNVRLAWFLSHLHQTVQATPQEMLLQSEQELEV
LSVLPPGWQPDEPVVPRPFLLVPSTRVTFLAWQYRFVIELDLSPSTGIVDDSTGEILFDE
VFHALSRCLGGLLRPFRVPGSCIDFQPEIYVTIQAYSSIIGLQSHQVLVQGCLLDPSQRE
VFLQQIYEQLCLFEDKVATMLQQQYDPQSQAEDQSPDSGDLLGRKVGVSMVTADLGLVSM
IRQGILALQLLPSNSSAGIIVITDGVTSVPDVAVCETLLNQLRSGTVACSFVQVGGVYSY
DCSFGHVPNVELMKFIAMATFGSYLSTCPEPEPGNLGLTVYHRAFLLYSFLRSGEALNPE
YYCGSQHRLFNEHLVSASSNPALALRRKKHTEKEVPADLVSTVSVRLREGYSVREVTLAK
GGSQLEVKLVLLWKHNMRIEYVAMAPWPLEPEGPRVTRVEVTMEGGYDILHDVSCALRQP
IRSLYRTHVIRRFWNTLQSINQTDQMLAHLQSFSSVPEHFTLPDSTKSGVPLFYIPPGST
TPVLSLQPSGSDSSHAQFAAYWKPVLSMDANSWQRWLHMHRLVLILEHDTPIPKHLHTPG
SNGRYSTIQCRISHSSLTSLLRDWSSFVLVEGYSYVKLLSSAPDQPPNSFYMVRIISKAP
CMVLRLGFPIGTPAPARHKIVSGLREEILRLRFPHRVQSKEPTPKVKRKGLGGAGGGSSP
SKSPPVLGPQQALSDRPCLVVLHKPLDKLLIRYEKLPLDYRAPFLLTLEPPGPLPLVSGR
SASSSLASLSRYLYHQRWLWSVPSGLAPALPLSAIAQLLSILTEVRLSEGFHFACSGEGI
INMVLELPIQNEPPGQAAAEEKHTCVVQYILFPPHSTSTKDSFSTDDDNDVEVEALEGDS
ELNLVTEVWVEPQYGRVGPGPGIWKHLQDLTYSEIPQALHPRDAACIGSMLSFEYLIQLC
QSKEWGPLPPEPRVSDGLDQGGDTCVHEIPFHFDLMGLLPQCQQLQMFFLLLAREPEGVP
FAEGSCPANDMVLCLLHSCLGQELSDREIPLTPVDQAAFLSEVLRRTCHVPGAEGPLLGV
HGIPKEQAVGSTQATGDSAFTSLSVGLPETLKPLISAQPPQWRCYARLVNPQHVFLTFLP
ATFSDVQRLAACGLEGPPQEETKPKFGDWSGAPSLKDLGGTGIKATKSHVPVLSVTLASD
NAQNQGELSPPFRRDLQAYAGRQASQTESADGPRTRCPVYIYSCSLEALREQMVGMQPPQ
APRDLIFRTQFLDHPSPSSAWMEPRYKEAANHCALLQEHAQRCYVRGLFRSLQQAQSVTS
QDLLTAVDACEELLQEIDITPFLLALCGHTWGLPHAPPSPGPLSPGPFSSSMEEGAEPRE
RAILASESSIETEDLSEPEFQSTRVPGIPDPGPEISLTDVCQLRGEAHGALHSVIQEKFL
EISRLHFRTVPSNPHYFFYCPPSSRREDEGPRDTVDRKISDLEFSEAELMGEEGDTSACC
VVTESDPELEVEYRESRESDLGPAGLDSASLSDVDTVNPDEDSFSILGGDSPTGPESFLH
DLPPLFLHLTCSVRLRGQHSSVPVCSLPTCLGQVLSSLEGPPVGGRVPLRDLSVTLDVFM
LTLPLEVELPTASDPQHHRSTSESSASFPRSPGQPSSLRSDDGLGPPLPPPEEERHPGLS
NLATPHRLAIETTMNEIRWLLEDEMVGALRRGGIPQSPALHRAAAHIHSSPGRSTCLRQT
LPLSFVFGPERSLTQFKEEFRRLHLPGHVLLEDPDSGFFFVAAGQQPGGSHGEPSSAAWA
WHSHEDRAEGIEGETLTASPQAPGSPEDSEGVPLISLPRVPQGGSQPGPSRGLSLMSSQG
SVDSDHLGYDGGSSGSDSEGPNDTLGEKAPFTLRTPPGPAPPQPSLSGLPGPCLPDFWLI
VRVLQDRVEVYAHARSLIREDGGPGTECRHLQQLLVRRVGEICREVNQRLLLQDLHDSHV
CNSLLVAESEEDLWRSETPFHSRQRAPLPSDDYAADESCAPRGYLAATMQFVPGHFSCDV
VWGTVIRVHSRLKMGPSMGVSRAIQALRSVLNAFSVVNRKNMFVYQERATKAVYYLRLLE
TSCSDRPWKGDALPPSLALSRSQEPIYSEEASGPRSPLDMVSSRSSDAARPVGQVDRHIQ
LLVHGVGQAGPEITDELVRVLCRRLDEATLDVITVMLVRNCKLTPADVEFIQPPGSLPSE
VLHLALPTSCRPWLPALAWYLRQNLLIFLHSPKYTDSNSRNHFQHPLPPQGGLPDLDIYL
YNKPGGQGTGGKGVACITLAFVDEGGAPLSLALWPPSSPGPPDPLREEEFEQLTQVIRCP
VVVDSSSAQNGAPRLRLDVWEKGNISIVQLEEKLRGAARQALADAIIELQLLPASLCTED
TPTGSLRNGSLETKSSAGRASTFPPAPVPGEPVTPPSKAGRRSFWDMLSKTECGDLGSPK
TTDDIVLDRPEDTRGRRRHKTESVRTPGGAERAPGSDSGAQRQKRRTTQLEEGEVGTLHP
VFARVAQRWMEFMVQIGCASVSRSSAHMVSRFLLPSILSEFTALVTSMAGDTSVRIFEQH
LGSEPEIFGPCSPGQLGPSPRPAAERHLLLLGRNFLQWRRPTQQAAKAMQRFEPGGDGSS
GRNAPRQRLLLLEVVDKKLQLLTYNWAPDLGAALGRALVRLVQWQNARAHLIFCLLSQKL
GLFHHYGQLDFPVRDEKEPNPFLLPTMEVETLIRSASPPLSREQGRLSGSSRGGGPLPLD
TFPFDEALRDITAARPSSVLGPVPRPPDPVTYHGQQFLEIKMAERRELERQMKMENLFVT
WQQRSTPATMPISAGELETLKQSSRLVHYCATAMLFDPAAWLHGPPETSGPPDGQRRHRP
ESGSGSREAPTSCESLDVSPPGAREEPWLKELSLAFLQQYVQYLQSIGFVLVPLRPPSPA
RSTSRPRAMAILGTEGRGSFSCPKTKTDGSPKSTSSPVTTYHLQRALPGGIILMELAFQG
CYFCVKQFALECSRIPMGQAVNSQLSMLFTEECDKVRDLMHVHSFSYDFHLRLVHQHVLG
AHLVLRHGYHLTTFLRHFLAHHPDGPHFGRNHIYQGTLELPTPLIAAHQLYNYVADHASS
YHMKPLRMARPGGPEHNEYALVSAWHSSGSYLDSEGLRHQDDFDVSLLVCHCAAPFEEQG
EAERHVLRLQFFVVLTSQRELFPRLTADMRRFRKPPRLPPEPEAPGSSAGSPGEASGLIL
APGPAPLFPPLAAEVGMARARLAQLVRLAGGHCRRDTLWKRLFLLEPPGPDRLRLGGRLA
LAELEELLEAVHAKSIGDIDPQLDCFLSMTVSWYQSLIKVLLSRFPQSCRHFQSPDLGTQ
YLVVLNQKFTDCFVLVFLDSHLGKTSLTVVFREPFPVQPQDSESPPAQLVSTYHHLESVI
NTACFTLWTRLL

Primary citation

Architecture of the human KICSTOR and GATOR1-KICSTOR complexes. Teng, F., Zeng, H., Mai, X. et al. Nat Struct Mol Biol (2025) 32:2587-2600. DOI 10.1038/s41594-025-01693-4 · PubMed

Other PDB entries of the same protein (UniProt Q8WTW4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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