9VAN: Human full length KICSTOR complex

Cryo-EM structure of human full length KICSTOR complex (state 2). Determined by electron microscopy at 2.9 Å resolution. Released 12 Nov 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 14,526
Mol. weight: 526.42 kDa
Released: 12 Nov 2025

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

Secondary structure: helices and β-sheets

9VAN contains 73 α-helices and 111 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: 43 helices, 46 β-strands

Element	Residues	Length	Sheet
α-helix	1717-1728	12
β-strand	1736	1	1
β-strand	1739	1	1
α-helix	1748-1750	3
α-helix	1753-1762	10
β-strand	1768-1772	5	1
β-strand	1779-1783	5	1
β-strand	1918-1923	6	1
β-strand	1928-1933	6	1
α-helix	1944-1978	35
α-helix	1990-1995	6
α-helix	2025-2030	6
β-strand	2040-2046	7	2
α-helix	2063-2070	8
α-helix	2072-2074	3
β-strand	2075	1	3
β-strand	2083	1	3
β-strand	2095-2099	5	2
β-strand	2159-2164	6	2
α-helix	2171-2174	4
α-helix	2176-2196	21
α-helix	2205-2211	7
β-strand	2222-2225	4	4
α-helix	2228-2230	3
α-helix	2234-2245	12
β-strand	2250	1	5
β-strand	2279-2282	4	5
α-helix	2283-2285	3
β-strand	2287	1	6
β-strand	2289	1	6
β-strand	2293-2297	5	5
α-helix	2330-2333	4
β-strand	2354-2357	4	4
β-strand	2359	1	5
β-strand	2362-2363	2	5
α-helix	2371-2386	16
α-helix	2387-2391	5
α-helix	2507-2510	4
α-helix	2521-2525	5
α-helix	2530-2533	4
β-strand	2544-2545	2	7
α-helix	2551-2553	3
α-helix	2554-2568	15
β-strand	2574-2579	6	7
β-strand	2588-2590	3	7
β-strand	2608-2612	5	7
α-helix	2615-2617	3
β-strand	2650	1	7
β-strand	2653-2655	3	7
β-strand	2658-2661	4	7
α-helix	2668-2699	32
α-helix	2729-2734	6
α-helix	2789-2805	17
α-helix	2809-2821	13
β-strand	2832	1	8
α-helix	2834-2843	10
β-strand	2848-2853	6	9
α-helix	2907-2925	19
β-strand	2930-2931	2	9
α-helix	2933	1
β-strand	2934	1	8
α-helix	2935-2936	2
β-strand	2981-2987	7	9
β-strand	2990-2999	10	9
β-strand	3002-3007	6	9
β-strand	3010	1	9
α-helix	3024-3038	15
α-helix	3042-3056	15
α-helix	3071-3081	11
β-strand	3092-3097	6	10
α-helix	3108-3116	9
α-helix	3118-3121	4
β-strand	3127	1	11
β-strand	3139	1	11
β-strand	3141-3147	7	10
β-strand	3163-3171	9	10
β-strand	3189-3196	8	10
α-helix	3249-3265	17
α-helix	3302-3309	8
β-strand	3312-3315	4	12
α-helix	3316-3319	4
α-helix	3321-3328	8
α-helix	3331-3344	14
β-strand	3349-3353	5	12
β-strand	3359-3365	7	12
β-strand	3372-3379	8	12
β-strand	3386-3391	6	12
α-helix	3394-3396	3
α-helix	3410-3430	21

Chain B: 3 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	13
β-strand	9-13	5	14
β-strand	23-26	4	15
β-strand	35-39	5	15
β-strand	44-48	5	15
β-strand	57-60	4	15
β-strand	65-71	7	16
β-strand	80-85	6	16
β-strand	90-93	4	16
β-strand	119-120	2	16
β-strand	127-133	7	17
β-strand	142-147	6	17
β-strand	151-158	8	17
β-strand	170-178	9	17
β-strand	186-190	5	18
β-strand	196-202	7	18
β-strand	206-210	5	18
β-strand	240-244	5	18
β-strand	256-260	5	19
β-strand	264	1	20
β-strand	275-280	6	19
β-strand	284-289	6	19
β-strand	296-302	7	19
β-strand	307-313	7	13
β-strand	320	1	20
β-strand	322-327	6	13
β-strand	331-335	5	13
β-strand	341-345	5	13
β-strand	350-359	10	14
β-strand	365-373	9	14
β-strand	377-381	5	14
α-helix	395-400	6
α-helix	402-410	9
α-helix	418-430	13

Chain C: 7 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	14-21	8	21
β-strand	31-32	2	22
β-strand	41-44	4	22
β-strand	50-58	9	22
β-strand	61-69	9	22
β-strand	79-87	9	23
β-strand	95-105	11	23
β-strand	108-116	9	23
α-helix	127-130	4
β-strand	137-138	2	23
β-strand	146-153	8	24
β-strand	156-164	9	24
β-strand	170-176	7	24
β-strand	181-185	5	24
α-helix	192-194	3
β-strand	201-208	8	25
β-strand	214-221	8	25
β-strand	225-232	8	25
β-strand	238-245	8	25
β-strand	250-256	7	26
β-strand	274-279	6	26
β-strand	285-288	4	26
α-helix	290-293	4
β-strand	298-300	3	26
α-helix	301	1
β-strand	310-316	7	27
β-strand	325-330	6	27
β-strand	334-341	8	27
α-helix	343-345	3
β-strand	353-358	6	27
β-strand	361	1	27
β-strand	366-372	7	21
α-helix	379-380	2
β-strand	381-386	6	21
β-strand	389-395	7	21
α-helix	397-419	23

Chain D: 20 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	13-26	14
α-helix	30-43	14
α-helix	49-70	22
α-helix	91-106	16
α-helix	110-112	3
α-helix	116-149	34
α-helix	157-170	14
α-helix	181-205	25
α-helix	209-241	33
α-helix	246-248	3
α-helix	250-252	3
α-helix	253-272	20
α-helix	274-278	5
α-helix	283-292	10
α-helix	297-308	12
β-strand	312-317	6	28
β-strand	348-352	5	28
α-helix	356-357	2
α-helix	361-370	10
α-helix	372-376	5
β-strand	381-386	6	28
β-strand	391-399	9	28
β-strand	402-408	7	28
α-helix	417-431	15
α-helix	433-438	6

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

>9VAN_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

>9VAN_2 KICSTOR complex protein ITFG2 (chains B)
MRSVSYVQRVALEFSGSLFPHAICLGDVDNDTLNELVVGDTSGKVSVYKNDDSRPWLTCS
CQGMLTCVGVGDVCNKGKNLLVAVSAEGWFHLFDLTPAKVLDASGHHETLIGEEQRPVFK
QHIPANTKVMLISDIDGDGCRELVVGYTDRVVRAFRWEELGEGPEHLTGQLVSLKKWMLE
GQVDSLSVTLGPLGLPELMVSQPGCAYAILLCTWKKDTGSPPASEGPTDGSRETPAARDV
VLHQTSGRIHNKNVSTHLIGNIKQGHGTESSGSGLFALCTLDGTLKLMEEMEEADKLLWS
VQVDHQLFALEKLDVTGNGHEEVVACAWDGQTYIIDHNRTVVRFQVDENIRAFCAGLYAC
KEGRNSPCLVYVTFNQKIYVYWEVQLERMESTNLVKLLETKPEYHSLLQELGVDPDDLPV
TRALLHQTLYHPDQPPQCAPSSLQDPT

Sequence of entity 3 (C), FASTA

>9VAN_3 KICSTOR complex protein kaptin (chains C)
MMGEAAVAAGPCPLREDSFTRFSSQSNVYGLAGGAGGRGELLAATLKGKVLGFRYQDLRQ
KIRPVAKELQFNYIPVDAEIVSIDTFNKSPPKRGLVVGITFIKDSGDKGSPFLNIYCDYE
PGSEYNLDSIAQSCLNLELQFTPFQLCHAEVQVGDQLETVFLLSGNDPAIHLYKENEGLH
QFEEQPVENLFPELTNLTSSVLWLDVHNFPGTSRRLSALGCQSGYVRVAHVDQRSREVLQ
MWSVLQDGPISRVIVFSLSAAKETKDRPLQDEYSVLVASMLEPAVVYRDLLNRGLEDQLL
LPGSDQFDSVLCSLVTDVDLDGRPEVLVATYGQELLCYKYRGPESGLPEAQHGFHLLWQR
SFSSPLLAMAHVDLTGDGLQELAVVSLKGVHILQHSLIQASELVLTRLRHQVEQRRRRLQ
GLEDGAGAGPAENAAS

Sequence of entity 4 (D), FASTA

>9VAN_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:

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)
9V9N 3.08 Å, Cryo-EM structure of KICSTOR CCC complex (state 5)
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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