9V9N: KICSTOR CCC complex

Cryo-EM structure of KICSTOR CCC complex (state 5). Determined by electron microscopy at 3.08 Å resolution. Released 12 Nov 2025.

Method: Electron microscopy
Resolution: 3.08 Å
Organism: Homo sapiens
Chains: 4
Atoms: 13,390
Mol. weight: 526.42 kDa
Released: 12 Nov 2025

Explore 9V9N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9V9N contains 59 α-helices and 101 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: 31 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	2222	1	1
α-helix	2228-2230	3
α-helix	2234-2248	15
β-strand	2250	1	2
β-strand	2278-2279	2	1
β-strand	2280	1	2
β-strand	2297-2302	6	1
β-strand	2354-2359	6	1
α-helix	2371-2386	16
α-helix	2387-2391	5
α-helix	2504-2512	9
α-helix	2521-2525	5
α-helix	2526-2532	7
α-helix	2553-2568	16
β-strand	2572-2575	4	3
β-strand	2581	1	4
β-strand	2583	1	4
β-strand	2607-2614	8	3
α-helix	2615-2617	3
β-strand	2630	1	5
β-strand	2650-2655	6	3
β-strand	2659-2662	4	3
β-strand	2666	1	5
α-helix	2668-2689	22
α-helix	2693-2699	7
α-helix	2764-2766	3
α-helix	2790-2793	4
α-helix	2797-2800	4
α-helix	2808-2822	15
β-strand	2832	1	6
α-helix	2834-2842	9
β-strand	2845-2853	9	7
α-helix	2858-2860	3
α-helix	2907-2925	19
β-strand	2930-2931	2	7
β-strand	2934	1	6
β-strand	2981-2986	6	7
β-strand	2990-2999	10	7
β-strand	3002-3011	10	7
α-helix	3027-3030	4
α-helix	3033-3038	6
α-helix	3042-3059	18
α-helix	3071-3081	11
β-strand	3092-3100	9	8
α-helix	3107-3116	10
β-strand	3124	1	8
β-strand	3127	1	9
β-strand	3139	1	9
β-strand	3141-3146	6	8
β-strand	3164-3170	7	8
α-helix	3183-3185	3
β-strand	3187-3195	9	8
α-helix	3249-3267	19
α-helix	3271-3281	11
α-helix	3300-3309	10
β-strand	3312-3315	4	10
α-helix	3316-3318	3
α-helix	3322-3328	7
α-helix	3331-3344	14
β-strand	3349-3353	5	10
β-strand	3359-3364	6	10
β-strand	3372-3379	8	10
β-strand	3384-3386	3	10
β-strand	3388-3391	4	10
α-helix	3410-3431	22

Chain B: 4 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	11
β-strand	9-13	5	12
β-strand	23-26	4	13
β-strand	35-39	5	13
β-strand	44-48	5	13
β-strand	57-60	4	13
β-strand	65-71	7	14
β-strand	80-85	6	14
β-strand	91-92	2	14
β-strand	119-120	2	14
β-strand	127-133	7	15
β-strand	142-147	6	15
β-strand	151-158	8	15
β-strand	170-178	9	15
β-strand	186-190	5	16
β-strand	196-202	7	16
β-strand	206-210	5	16
α-helix	211-213	3
β-strand	240-244	5	16
β-strand	256-259	4	17
β-strand	275-280	6	17
β-strand	284-289	6	17
β-strand	296-302	7	17
β-strand	307	1	18
β-strand	311-313	3	11
β-strand	322-325	4	11
β-strand	327	1	18
β-strand	331-335	5	11
β-strand	341-345	5	11
β-strand	350-359	10	12
β-strand	365-373	9	12
β-strand	377-381	5	12
α-helix	394-398	5
α-helix	402-410	9
α-helix	418-430	13

Chain C: 5 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	14-21	8	19
β-strand	26-32	7	20
β-strand	41-45	5	20
β-strand	50-58	9	20
β-strand	61-69	9	20
β-strand	79-87	9	21
β-strand	95-103	9	21
β-strand	110-116	7	21
α-helix	127-131	5
β-strand	135-138	4	21
β-strand	146-153	8	22
β-strand	156-164	9	22
β-strand	170-175	6	22
β-strand	182-185	4	22
β-strand	201-208	8	23
β-strand	214-221	8	23
β-strand	225-232	8	23
β-strand	237-245	9	23
β-strand	250-257	8	24
β-strand	273-279	7	24
β-strand	285-288	4	24
α-helix	290-293	4
β-strand	297-300	4	24
α-helix	301	1
β-strand	310-316	7	25
β-strand	325-330	6	25
β-strand	334	1	26
β-strand	335-341	7	25
α-helix	343-345	3
β-strand	353-358	6	25
β-strand	361	1	26
β-strand	366-369	4	19
β-strand	372	1	27
β-strand	381	1	27
β-strand	382-386	5	19
β-strand	389-395	7	19
α-helix	397-412	16

Chain D: 19 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	21-25	5
α-helix	31-43	13
α-helix	51-70	20
α-helix	95-97	3
α-helix	99-103	5
α-helix	117-149	33
α-helix	157-170	14
α-helix	181-203	23
α-helix	204-206	3
α-helix	209-223	15
α-helix	224-228	5
α-helix	253-272	20
α-helix	275-279	5
α-helix	286-289	4
α-helix	297-307	11
β-strand	314-317	4	28
α-helix	366-369	4
α-helix	372-375	4
β-strand	381	1	28
β-strand	396	1	28
β-strand	402-405	4	28
α-helix	417-427	11
α-helix	434-437	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
KICSTOR complex protein SZT2	A	protein	3432	Homo sapiens	Q5T011 (AlphaFold model)
KICSTOR complex protein ITFG2	B	protein	447	Homo sapiens	Q969R8 (AlphaFold model)
KICSTOR complex protein kaptin	C	protein	436	Homo sapiens	Q9Y664 (AlphaFold model)
KICSTOR subunit 2	D	protein	445	Homo sapiens	Q96MD2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9V9N_1 KICSTOR complex protein SZT2 (chains A)
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

Sequence of entity 2 (B), FASTA

>9V9N_2 KICSTOR complex protein ITFG2 (chains B)
MRSVSYVQRVALEFSGSLFPHAICLGDVDNDTLNELVVGDTSGKVSVYKNDDSRPWLTCS
CQGMLTCVGVGDVCNKGKNLLVAVSAEGWFHLFDLTPAKVLDASGHHETLIGEEQRPVFK
QHIPANTKVMLISDIDGDGCRELVVGYTDRVVRAFRWEELGEGPEHLTGQLVSLKKWMLE
GQVDSLSVTLGPLGLPELMVSQPGCAYAILLCTWKKDTGSPPASEGPTDGSRETPAARDV
VLHQTSGRIHNKNVSTHLIGNIKQGHGTESSGSGLFALCTLDGTLKLMEEMEEADKLLWS
VQVDHQLFALEKLDVTGNGHEEVVACAWDGQTYIIDHNRTVVRFQVDENIRAFCAGLYAC
KEGRNSPCLVYVTFNQKIYVYWEVQLERMESTNLVKLLETKPEYHSLLQELGVDPDDLPV
TRALLHQTLYHPDQPPQCAPSSLQDPT

Sequence of entity 3 (C), FASTA

>9V9N_3 KICSTOR complex protein kaptin (chains C)
MMGEAAVAAGPCPLREDSFTRFSSQSNVYGLAGGAGGRGELLAATLKGKVLGFRYQDLRQ
KIRPVAKELQFNYIPVDAEIVSIDTFNKSPPKRGLVVGITFIKDSGDKGSPFLNIYCDYE
PGSEYNLDSIAQSCLNLELQFTPFQLCHAEVQVGDQLETVFLLSGNDPAIHLYKENEGLH
QFEEQPVENLFPELTNLTSSVLWLDVHNFPGTSRRLSALGCQSGYVRVAHVDQRSREVLQ
MWSVLQDGPISRVIVFSLSAAKETKDRPLQDEYSVLVASMLEPAVVYRDLLNRGLEDQLL
LPGSDQFDSVLCSLVTDVDLDGRPEVLVATYGQELLCYKYRGPESGLPEAQHGFHLLWQR
SFSSPLLAMAHVDLTGDGLQELAVVSLKGVHILQHSLIQASELVLTRLRHQVEQRRRRLQ
GLEDGAGAGPAENAAS

Sequence of entity 4 (D), FASTA

>9V9N_4 KICSTOR subunit 2 (chains D)
MGESIPLAAPVPVEQAVLETFFSHLGIFSYDKAKDNVEKEREANKSAGGSWLSLLAALAH
LAAAEKVYHSLTYLGQKLGGQSFFSRKDSIRTIYTSLHNELKKVVTGRGALGGTAPHVEE
LLSHLSEQLCFFVQARMEIADFYEKMYTLSTQKFINAEELVGLLDAIMKKYSSRFHHPIL
SPLESSFQLEVDVLCHLLKAQAQVSEWKFLPSLVNLHSAHTKLQTWGQIFEKQRETKKHL
FGGQSQKAVQPPHLFLWLMKLKNMLLAKFSFYFHEALSRQTTASEMKTLTAKANPDFFGK
ISSFIRKYDAANVSLIFDNRGSESFQGHGYHHPHSYREAPKGVDQYPAVVSLPSDRPVMH
WPNVIMIMTDRTSDLNSLEKVVHFYDDKVQSTYFLTRPEPHFTIVIIFESKKSERDSHFI
SFLNEVSLALKNPKVFASLKPGAKG

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 Q5T011 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9VAN 2.9 Å, Cryo-EM structure of human full length KICSTOR complex (state 2)
9V80 2.95 Å, Cryo-EM structure of KICSTOR CCC complex (state 4)
9V0J 2.97 Å, Cryo-EM structure of GATOR1-KICSTOR complex
9V86 3.04 Å, Cryo-EM structure of KICSTOR CCC complex (state 3)
9V6E 3.19 Å, Cryo-EM structure of human full length KICSTOR complex (state 1)
9O5A 3.2 Å, The KICSTOR-GATOR1 complex
9O5D 3.34 Å, The KICSTOR-GATOR1-SAMTOR complex
25GE 3.37 Å, Cryo-EM structure of the human KPTN-ITFG2-SZT2(2189-3432) complex
25GF 3.81 Å, Cryo-EM structure of the human KPTN-ITFG2-C12orf66-SZT2(2189-3432) complex
9O5E 5.0 Å, The dimeric KICSTOR-GATOR1 supercomplex

Browse structure collections

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