9XZY: DEPDC5 dimer (tandem DEPDC5) focused map

DEPDC5 dimer (tandem DEPDC5) focused map. Determined by electron microscopy at 3.8 Å resolution. Released 11 Feb 2026.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Homo sapiens
Chains: 1
Atoms: 15,736
Mol. weight: 379.24 kDa
Released: 11 Feb 2026

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

Secondary structure: helices and β-sheets

9XZY contains 84 α-helices and 118 β-strands across 1 chain. 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 H: 84 helices, 118 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	1
β-strand	8-12	5	2
β-strand	23-25	3	2
β-strand	38-42	5	3
α-helix	50	1
β-strand	51-54	4	3
β-strand	58	1	2
α-helix	63	1
β-strand	66-70	5	2
α-helix	71-76	6
β-strand	85	1	1
β-strand	86-89	4	3
β-strand	96	1	4
β-strand	99-104	6	5
α-helix	111-121	11
β-strand	124-127	4	4
β-strand	131-134	4	5
β-strand	137-141	5	5
β-strand	144-146	3	5
β-strand	149-151	3	5
β-strand	153-156	4	4
β-strand	161-166	6	5
β-strand	170-176	7	6
α-helix	179-182	4
β-strand	184	1	7
β-strand	190	1	7
α-helix	191-194	4
α-helix	195-200	6
α-helix	201-209	9
β-strand	215-226	12	6
α-helix	231-233	3
α-helix	239-241	3
β-strand	242-244	3	6
β-strand	250-262	13	6
α-helix	268-284	17
α-helix	294-295	2
β-strand	296-298	3	6
α-helix	299-300	2
α-helix	306-317	12
β-strand	322	1	8
β-strand	331-337	7	6
β-strand	342-345	4	9
α-helix	347-360	14
α-helix	363-364	2
β-strand	365-368	4	6
β-strand	379-382	4	9
β-strand	397-398	2	9
β-strand	404-407	4	6
α-helix	744-748	5
α-helix	750	1
β-strand	751	1	5
α-helix	752-754	3
β-strand	756	1	10
α-helix	763-769	7
β-strand	770-776	7	10
α-helix	795-809	15
β-strand	812-813	2	10
β-strand	851-856	6	10
β-strand	859-865	7	10
β-strand	870-877	8	10
α-helix	880	1
β-strand	881-893	13	6
α-helix	901	1
β-strand	902-909	8	6
α-helix	918-926	9
β-strand	942-950	9	8
α-helix	953-960	8
α-helix	969-971	3
α-helix	973-975	3
α-helix	976-993	18
β-strand	1172	1	11
α-helix	1179-1184	6
β-strand	1204-1206	3	12
α-helix	1207-1217	11
β-strand	1219	1	11
α-helix	1224-1236	13
β-strand	1240-1242	3	12
α-helix	1247-1249	3
β-strand	1254-1255	2	13
β-strand	1257-1260	4	12
α-helix	1287-1290	4
β-strand	1296-1298	3	13
β-strand	1352-1358	7	8
β-strand	1369-1375	7	8
β-strand	1377-1378	2	13
β-strand	1384-1390	7	8
α-helix	1395-1411	17
β-strand	1414-1419	6	8
β-strand	1439-1442	4	14
α-helix	1445-1448	4
α-helix	1462-1464	3
α-helix	1465-1478	14
β-strand	1482-1485	4	14
β-strand	1501-1504	4	14
β-strand	1509-1512	4	14
α-helix	1519-1525	7
β-strand	1545-1550	6	14
α-helix	1556-1558	3
α-helix	1567-1580	14
α-helix	1583-1585	3
α-helix	1586-1595	10
β-strand	1770	1	15
β-strand	1771-1775	5	16
β-strand	1786-1788	3	16
β-strand	1801-1805	5	17
α-helix	1813	1
β-strand	1814-1817	4	17
β-strand	1821	1	16
α-helix	1826	1
β-strand	1829-1833	5	16
α-helix	1834-1839	6
β-strand	1848	1	15
β-strand	1849-1852	4	17
β-strand	1859	1	18
β-strand	1862-1867	6	19
α-helix	1874-1884	11
β-strand	1887-1890	4	18
β-strand	1894-1897	4	19
β-strand	1900-1904	5	19
β-strand	1907-1909	3	19
β-strand	1912-1914	3	19
β-strand	1916-1919	4	18
β-strand	1924-1929	6	19
β-strand	1933-1939	7	6
α-helix	1942-1945	4
β-strand	1947	1	20
β-strand	1953	1	20
α-helix	1954-1957	4
α-helix	1958-1963	6
α-helix	1964-1972	9
β-strand	1978-1989	12	6
α-helix	1994-1996	3
α-helix	2002-2004	3
β-strand	2005-2007	3	6
β-strand	2013-2025	13	6
α-helix	2031-2047	17
α-helix	2057-2058	2
β-strand	2059-2061	3	6
α-helix	2062-2063	2
α-helix	2069-2080	12
β-strand	2085	1	21
β-strand	2094-2100	7	6
β-strand	2105-2108	4	22
α-helix	2110-2123	14
α-helix	2126-2127	2
β-strand	2128-2131	4	6
β-strand	2142-2145	4	22
β-strand	2160-2161	2	22
β-strand	2167-2170	4	6
α-helix	2507-2511	5
α-helix	2513	1
β-strand	2514	1	19
α-helix	2515-2517	3
β-strand	2519	1	23
α-helix	2526-2532	7
β-strand	2533-2539	7	23
α-helix	2558-2572	15
β-strand	2575-2576	2	23
β-strand	2614-2619	6	23
β-strand	2622-2628	7	23
β-strand	2633-2640	8	23
α-helix	2643	1
β-strand	2644-2656	13	6
α-helix	2664	1
β-strand	2665-2672	8	6
α-helix	2681-2689	9
β-strand	2705-2713	9	21
α-helix	2716-2723	8
α-helix	2732-2734	3
α-helix	2736-2738	3
α-helix	2739-2756	18
β-strand	2935	1	24
α-helix	2942-2947	6
β-strand	2967-2969	3	25
α-helix	2970-2980	11
β-strand	2982	1	24
α-helix	2987-2999	13
β-strand	3003-3005	3	25
α-helix	3010-3012	3
β-strand	3017-3018	2	26
β-strand	3020-3023	4	25
α-helix	3050-3053	4
β-strand	3059-3061	3	26
β-strand	3115-3121	7	21
β-strand	3132-3138	7	21
β-strand	3140-3141	2	26
β-strand	3147-3153	7	21
α-helix	3158-3174	17
β-strand	3177-3182	6	21
β-strand	3202-3205	4	27
α-helix	3208-3211	4
α-helix	3225-3227	3
α-helix	3228-3241	14
β-strand	3245-3248	4	27
β-strand	3264-3267	4	27
β-strand	3272-3275	4	27
α-helix	3282-3288	7
β-strand	3308-3313	6	27
α-helix	3319-3321	3
α-helix	3330-3343	14
α-helix	3346-3348	3
α-helix	3349-3358	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GATOR1 complex protein DEPDC5	H	protein	3384	Homo sapiens	O75140 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>9XZY_1 GATOR1 complex protein DEPDC5 (chains H)
MGDYKDDDDKGGGGGASTMRTTKVYKLVIHKKGFGGSDDELVVNPKVFPHIKLGDIVEIA
HPNDEYSPLLLQVKSLKEDLQKETISVDQTVTQVFRLRPYQDVYVNVVDPKDVTLDLVEL
TFKDQYIGRGDMWRLKKSLVSTCAYITQKVEFAGIRAQAGELWVKNEKVMCGYISEDTRV
VFRSTSAMVYIFIQMSCEMWDFDIYGDLYFEKAVNGFLADLFTKWKEKNCSHEVTVVLFS
RTFYDAKSVDEFPEINRASIRQDHKGRFYEDFYKVVVQNERREEWTSLLVTIKKLFIQYP
VLVRLEQAEGFPQGDNSTSAQGNYLEAINLSFNVFDKHYINRNFDRTGQMSVVITPGVGV
FEVDRLLMILTKQRMIDNGIGVDLVCMGEQPLHAVPLFKLHNRSAPRDSRLGDDYNIPHW
INHSFYTSKSQLFCNSFTPRIKLAGKKPASEKAKNGRDTSLGSPKESENALPIQVDYDAY
DAQVFRLPGPSRAQCLTTCRSVRERESHSRKSASSCDVSSSPSLPSRTLPTEEVRSQASD
DSSLGKSANILMIPHPHLHQYEVSSSLGYTSTRDVLENMMEPPQRDSSAPGRFHVGSAES
MLHVRPGGYTPQRALINPFAPSRMPMKLTSNRRRWMHTFPVGPSGEAIQIHHQTRQNMAE
LQGSGQRDPTHSSAELLELAYHEAAGRHSNSRQPGDGMSFLNFSGTEELSVGLLSNSGAG
MNPRTQNKDSLEDSVSTSPDPILTLSAPPVVPGFCCTVGVDWKSLTTPACLPLTTDYFPD
RQGLQNDYTEGCYDLLPEADIDRRDEDGVQMTAQQVFEEFICQRLMQGYQIIVQPKTQKP
NPAVPPPLSSSPLYSRGLVSRNRPEEEDQYWLSMGRTFHKVTLKDKMITVTRYLPKYPYE
SAQIHYTYSLCPSHSDSEFVSCWVEFSHERLEEYKWNYLDQYICSAGSEDFSLIESLKFW
RTRFLLLPACVTATKRITEGEAHCDIYGDRPRADEDEWQLLDGFVRFVEGLNRIRRRHRS
DRMMRKGTAMKGLQMTGPISTHSLESTAPPVGKKGTSALSALLEMEASQKCLGEQQAAVH
GGKSSAQSAESSSVAMTPTYMDSPRKDGAFFMEFVRSPRTASSAFYPQVSVDQTATPMLD
GTSLGICTGQSMDRGNSQTFGNSQNIGEQGYSSTNSSDSSSQQLVASSLTSSSTLTEILE
AMKHPSTGVQLLSEQKGLSPYCFISAEVVHWLVNHVEGIQTQAMAIDIMQKMLEEQLITH
ASGEAWRTFIYGFYFYKIVTDKEPDRVAMQQPATTWHTAGVDDFASFQRKWFEVAFVAEE
LVHSEIPAFLLPWLPSRPASYASRHSSFSRSFGGRSQAAALLAATVPEQRTVTLDVDVNN
RTDRLEWCSCYYHGNFSLNAAFEIKLHWMAVTAAVLFEMVQGWHRKATSCGFLLVPVLEG
PFALPSYLYGDPLRAQLFIPLNISCLLKEGSEHLFDSFEPETYWDRMHLFQEAIAHRFGF
VQDKYSASAFNFPAENKPQYIHVTGTVFLQLPYSKRKFSGQQRRRRNSTSSTNQNMFCEE
RVGYNWAYNTMLTKTWRSSATGDEKFADRLLKDFTDFCINRDNRLVTFWTSCLEKMHASA
PGGASGSYYRAEKGQGSGAEPQSGHSSRGSGSFVKFFTYSTQPTGSGGGMASMGHTGLKG
GSGGDSQCGTSMSGQESGQGGGGGQGGDGGVGLSGIGGGAGATDSGIPGLGVSGGENGGK
ASPGGTPAPKMMTTQSTCGFNGGSTGLGGTGSGQMGKGRSTMRTTKVYKLVIHKKGFGGS
DDELVVNPKVFPHIKLGDIVEIAHPNDEYSPLLLQVKSLKEDLQKETISVDQTVTQVFRL
RPYQDVYVNVVDPKDVTLDLVELTFKDQYIGRGDMWRLKKSLVSTCAYITQKVEFAGIRA
QAGELWVKNEKVMCGYISEDTRVVFRSTSAMVYIFIQMSCEMWDFDIYGDLYFEKAVNGF
LADLFTKWKEKNCSHEVTVVLFSRTFYDAKSVDEFPEINRASIRQDHKGRFYEDFYKVVV
QNERREEWTSLLVTIKKLFIQYPVLVRLEQAEGFPQGDNSTSAQGNYLEAINLSFNVFDK
HYINRNFDRTGQMSVVITPGVGVFEVDRLLMILTKQRMIDNGIGVDLVCMGEQPLHAVPL
FKLHNRSAPRDSRLGDDYNIPHWINHSFYTSKSQLFCNSFTPRIKLAGKKPASEKAKNGR
DTSLGSPKESENALPIQVDYDAYDAQVFRLPGPSRAQCLTTCRSVRERESHSRKSASSCD
VSSSPSLPSRTLPTEEVRSQASDDSSLGKSANILMIPHPHLHQYEVSSSLGYTSTRDVLE
NMMEPPQRDSSAPGRFHVGSAESMLHVRPGGYTPQRALINPFAPSRMPMKLTSNRRRWMH
TFPVGPSGEAIQIHHQTRQNMAELQGSGQRDPTHSSAELLELAYHEAAGRHSNSRQPGDG
MSFLNFSGTEELSVGLLSNSGAGMNPRTQNKDSLEDSVSTSPDPILTLSAPPVVPGFCCT
VGVDWKSLTTPACLPLTTDYFPDRQGLQNDYTEGCYDLLPEADIDRRDEDGVQMTAQQVF
EEFICQRLMQGYQIIVQPKTQKPNPAVPPPLSSSPLYSRGLVSRNRPEEEDQYWLSMGRT
FHKVTLKDKMITVTRYLPKYPYESAQIHYTYSLCPSHSDSEFVSCWVEFSHERLEEYKWN
YLDQYICSAGSEDFSLIESLKFWRTRFLLLPACVTATKRITEGEAHCDIYGDRPRADEDE
WQLLDGFVRFVEGLNRIRRRHRSDRMMRKGTAMKGLQMTGPISTHSLESTAPPVGKKGTS
ALSALLEMEASQKCLGEQQAAVHGGKSSAQSAESSSVAMTPTYMDSPRKDGAFFMEFVRS
PRTASSAFYPQVSVDQTATPMLDGTSLGICTGQSMDRGNSQTFGNSQNIGEQGYSSTNSS
DSSSQQLVASSLTSSSTLTEILEAMKHPSTGVQLLSEQKGLSPYCFISAEVVHWLVNHVE
GIQTQAMAIDIMQKMLEEQLITHASGEAWRTFIYGFYFYKIVTDKEPDRVAMQQPATTWH
TAGVDDFASFQRKWFEVAFVAEELVHSEIPAFLLPWLPSRPASYASRHSSFSRSFGGRSQ
AAALLAATVPEQRTVTLDVDVNNRTDRLEWCSCYYHGNFSLNAAFEIKLHWMAVTAAVLF
EMVQGWHRKATSCGFLLVPVLEGPFALPSYLYGDPLRAQLFIPLNISCLLKEGSEHLFDS
FEPETYWDRMHLFQEAIAHRFGFVQDKYSASAFNFPAENKPQYIHVTGTVFLQLPYSKRK
FSGQQRRRRNSTSSTNQNMFCEERVGYNWAYNTMLTKTWRSSATGDEKFADRLLKDFTDF
CINRDNRLVTFWTSCLEKMHASAP

Primary citation

Structure of the lysosomal KICSTOR-GATOR1 nutrient-sensing supercomplex. Bayly-Jones, C., Lupton, C.J., Chang, Y.G. et al. To be published.

Other PDB entries of the same protein (UniProt O75140 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9V0J 2.97 Å, Cryo-EM structure of GATOR1-KICSTOR complex
8FW5 3.08 Å, Chimeric HsGATOR1-SpGtr-SpLam complex
9O5A 3.2 Å, The KICSTOR-GATOR1 complex
9O5D 3.34 Å, The KICSTOR-GATOR1-SAMTOR complex
7T3B 3.9 Å, GATOR1-RAG-RAGULATOR - GAP Complex
6CES 4.0 Å, Cryo-EM structure of GATOR1-RAG
7T3A 4.0 Å, GATOR1-RAG-RAGULATOR - Inhibitory Complex
7T3C 4.0 Å, GATOR1-RAG-RAGULATOR - Dual Complex
6CET 4.4 Å, Cryo-EM structure of GATOR1
9O5E 5.0 Å, The dimeric KICSTOR-GATOR1 supercomplex

Browse structure collections

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