7T3C: GATOR1-RAG-RAGULATOR - Dual Complex

GATOR1-RAG-RAGULATOR - Dual Complex. Determined by electron microscopy at 4.0 Å resolution. Released 6 Apr 2022.

Method: Electron microscopy
Resolution: 4.0 Å
Organism: Homo sapiens
Chains: 17
Atoms: 32,452
Mol. weight: 582.76 kDa
Ligands: AF3, GDP
Released: 6 Apr 2022

Explore 7T3C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7T3C contains 159 α-helices and 188 β-strands across 17 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: 37 helices, 57 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	8
β-strand	8-12	5	9
β-strand	23-24	2	9
β-strand	25	1	10
β-strand	38-42	5	8
β-strand	50-54	5	8
β-strand	58	1	10
β-strand	66-70	5	9
α-helix	71-77	7
α-helix	79-80	2
β-strand	85-89	5	8
β-strand	96-97	2	11
β-strand	100-104	5	12
α-helix	111-120	10
β-strand	123-127	5	11
β-strand	131-133	3	12
β-strand	138-144	7	12
α-helix	146-148	3
β-strand	153-157	5	11
β-strand	163-165	3	12
β-strand	170-176	7	13
α-helix	179-181	3
β-strand	184	1	14
β-strand	190	1	14
α-helix	191-193	3
α-helix	194-200	7
α-helix	201-209	9
β-strand	215-225	11	13
β-strand	226	1	15
β-strand	239	1	13
β-strand	251-258	8	13
α-helix	269-280	12
α-helix	282-286	5
β-strand	294	1	15
α-helix	307-317	11
α-helix	318-320	3
β-strand	331-337	7	13
β-strand	344	1	16
α-helix	347-359	13
β-strand	364-367	4	13
β-strand	380-381	2	16
β-strand	397-398	2	16
β-strand	407	1	13
α-helix	744-748	5
α-helix	750	1
β-strand	751	1	12
α-helix	752-754	3
β-strand	756	1	17
α-helix	764-768	5
β-strand	770-777	8	17
α-helix	796-808	13
β-strand	812-813	2	17
β-strand	851-856	6	17
β-strand	859-865	7	17
β-strand	870-877	8	17
α-helix	880-882	3
β-strand	885-893	9	13
β-strand	902-909	8	13
α-helix	918-926	9
α-helix	937-939	3
β-strand	942-950	9	18
α-helix	953-960	8
α-helix	976-993	18
α-helix	1178-1185	8
α-helix	1191-1192	2
β-strand	1205	1	19
α-helix	1208-1217	10
α-helix	1225-1235	11
β-strand	1240-1241	2	20
β-strand	1254	1	21
β-strand	1258	1	19
β-strand	1259-1260	2	20
α-helix	1287-1290	4
β-strand	1297-1298	2	21
β-strand	1351-1357	7	18
β-strand	1369-1375	7	18
β-strand	1377-1378	2	21
β-strand	1382	1	22
β-strand	1384-1390	7	18
α-helix	1395-1410	16
β-strand	1414-1418	5	18
β-strand	1439-1441	3	22
α-helix	1445-1448	4
α-helix	1449-1450	2
α-helix	1465-1479	15
β-strand	1482-1485	4	22
α-helix	1499-1500	2
β-strand	1501-1504	4	22
β-strand	1509-1512	4	22
β-strand	1546-1550	5	22
α-helix	1556-1558	3
α-helix	1566-1580	15
α-helix	1583-1585	3
α-helix	1586-1594	9

Chain B: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	1
β-strand	16	1	2
β-strand	19	1	2
β-strand	24-26	3	1
α-helix	36-40	5
β-strand	55-58	4	1
β-strand	62-66	5	1
β-strand	69	1	1
β-strand	83-90	8	1
α-helix	99-116	18
α-helix	122-124	3
α-helix	125-139	15
β-strand	144-147	4	3
β-strand	155-158	4	3
α-helix	165-168	4
β-strand	174-177	4	4
α-helix	181-183	3
α-helix	186-188	3
α-helix	191-196	6
α-helix	197-199	3
α-helix	206-212	7
α-helix	217-230	14
β-strand	232-235	4	4
β-strand	244-247	4	5
α-helix	253-256	4
α-helix	259-263	5
α-helix	264-268	5
β-strand	269	1	6
α-helix	278-286	9
α-helix	294-300	7
β-strand	308	1	6
α-helix	310-319	10
β-strand	323-326	4	5
β-strand	328-329	2	7
α-helix	351-357	7
α-helix	363-369	7
β-strand	378-379	2	7

Chain C: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	1
β-strand	16	1	26
β-strand	22-26	5	1
α-helix	66-72	7
α-helix	77-79	3
β-strand	84-88	5	1
β-strand	91-95	5	1
β-strand	121	1	26
β-strand	125-131	7	1
α-helix	136-159	24
α-helix	162-173	12
α-helix	199-212	14
α-helix	223-225	3
β-strand	260	1	27
β-strand	263	1	28
α-helix	267-273	7
α-helix	280-288	9
α-helix	295-301	7
α-helix	306-318	13
β-strand	322	1	28
β-strand	325	1	27
β-strand	333-336	4	29
α-helix	348-355	8
α-helix	361-367	7
β-strand	372-373	2	29
α-helix	374-377	4
α-helix	384-399	16
β-strand	403-406	4	29
β-strand	407-411	5	30
α-helix	481-487	7
α-helix	492-498	7
α-helix	508-514	7
β-strand	521-525	5	30
α-helix	526-533	8
α-helix	537-546	10
β-strand	552-556	5	30
α-helix	559-563	5

Chain D: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	31
β-strand	14	1	32
α-helix	20-28	9
α-helix	33-36	4
β-strand	46-52	7	31
β-strand	56-62	7	31
α-helix	67-75	9
α-helix	78-82	5
β-strand	85-88	4	31
β-strand	91-92	2	32
α-helix	99-116	18
β-strand	121-122	2	31
β-strand	123	1	33
β-strand	125-127	3	32
α-helix	137-150	14
β-strand	158	1	33
β-strand	161-162	2	32
α-helix	168-180	13
α-helix	184-197	14
β-strand	202-206	5	34
α-helix	207	1
β-strand	213-218	6	34
α-helix	226-243	18
β-strand	251-255	5	34
β-strand	260-264	5	34
β-strand	271-275	5	34
α-helix	284-298	15

Chain E: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	64	1	35
α-helix	74-81	8
α-helix	89-92	4
β-strand	100-102	3	35
β-strand	114-116	3	35
α-helix	130-134	5
β-strand	140-145	6	35
α-helix	151-167	17
β-strand	173-178	6	35
α-helix	180-182	3
α-helix	185-204	20
β-strand	215-217	3	35
α-helix	224-236	13
α-helix	240-254	15
β-strand	258-262	5	34
α-helix	280-299	20
β-strand	315-319	5	34
β-strand	325-329	5	34
β-strand	336-341	6	34
α-helix	349-366	18

Chain F: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	50-61	12
α-helix	79-97	19
α-helix	105-107	3
α-helix	115-118	4
α-helix	126-145	20
β-strand	155	1	24

Chain G: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	24
α-helix	4-13	10
β-strand	21-25	5	23
β-strand	31	1	23
α-helix	45-63	19
β-strand	69-75	7	23
β-strand	79-86	8	23
β-strand	89-96	8	23
α-helix	101-113	13
α-helix	117-124	8

Chain H: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-11	9
α-helix	13-15	3
β-strand	19-25	7	23
β-strand	33-36	4	23
α-helix	42-44	3
α-helix	47-61	15
β-strand	70-75	6	23
β-strand	78-85	8	23
β-strand	88-95	8	23
α-helix	100-109	10
α-helix	111-117	7

9 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GATOR complex protein NPRL2	B	protein	380	Homo sapiens	Q8WTW4 (AlphaFold model)
GATOR complex protein DEPDC5	A	protein	1603	Homo sapiens	O75140 (AlphaFold model)
Ragulator complex protein LAMTOR3	H, O	protein	124	Homo sapiens	Q9UHA4 (AlphaFold model)
Ragulator complex protein LAMTOR2	G, N	protein	125	Homo sapiens	Q9Y2Q5 (AlphaFold model)
Ragulator complex protein LAMTOR5	J, Q	protein	91	Homo sapiens	O43504
Ragulator complex protein LAMTOR4	I, P	protein	99	Homo sapiens	Q0VGL1
Ragulator complex protein LAMTOR1	F, M	protein	161	Homo sapiens	Q6IAA8
GATOR complex protein NPRL3	C	protein	569	Homo sapiens	Q12980
Ras-related GTP-binding protein A	D, K	protein	313	Homo sapiens	Q7L523
Ras-related GTP-binding protein C	E	protein	399	Homo sapiens	Q9HB90
Ras-related GTP-binding protein C	L	protein	399	Homo sapiens	Q9HB90

Sequence of entity 1 (B), FASTA

>7T3C_1 GATOR complex protein NPRL2 (chains B)
MGSGCRIECIFFSEFHPTLGPKITYQVPEDFISRELFDTVQVYIITKPELQNKLITVTAM
EKKLIGCPVCIEHKKYSRNALLFNLGFVCDAQAKTCALEPIVKKLAGYLTTLELESSFVS
MEESKQKLVPIMTILLEELNASGRCTLPIDESNTIHLKVIEQRPDPPVAQEYDVPVFTKD
KEDFFNSQWDLTTQQILPYIDGFRHIQKISAEADVELNLVRIAIQNLLYYGVVTLVSILQ
YSNVYCPTPKVQDLVDDKSLQEACLSYVTKQGHKRASLRDVFQLYCSLSPGTTVRDLIGR
HPQQLQHVDERKLIQFGLMKNLIRRLQKYPVRVTREEQSHPARLYTGCHSYDEICCKTGM
SYHELDERLENDPNIIICWK

Sequence of entity 2 (A), FASTA

>7T3C_2 GATOR complex protein DEPDC5 (chains A)
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 3 (H, O), FASTA

>7T3C_3 Ragulator complex protein LAMTOR3 (chains H, O)
MADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQG
SKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQV
VEVS

Sequence of entity 4 (G, N), FASTA

>7T3C_4 Ragulator complex protein LAMTOR2 (chains G, N)
MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNG
NQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLT
QVAAS

Sequence of entity 5 (J, Q), FASTA

>7T3C_5 Ragulator complex protein LAMTOR5 (chains J, Q)
MEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPT
DIPVVCLESDNGNIMIQKHDGITVAVHKMAS

Sequence of entity 6 (I, P), FASTA

>7T3C_6 Ragulator complex protein LAMTOR4 (chains I, P)
MTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMN
VPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV

Sequence of entity 7 (F, M), FASTA

>7T3C_7 Ragulator complex protein LAMTOR1 (chains F, M)
MGCCYSSENEDSDQDREERKLLLDPSSPPTKALNGAEPNYHSLPSARTDEQALLSSILAK
TASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLA
SEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGIP

Sequence of entity 8 (C), FASTA

>7T3C_8 GATOR complex protein NPRL3 (chains C)
MRDNTSPISVILVSSGSRGNKLLFRYPFQRSQEHPASQTSKPRSRYAASNTGDHADEQDG
DSRFSDVILATILATKSEMCGQKFELKIDNVRFVGHPTLLQHALGQISKTDPSPKREAPT
MILFNVVFALRANADPSVINCLHNLSRRIATVLQHEERRCQYLTREAKLILALQDEVSAM
ADGNEGPQSPFHHILPKCKLARDLKEAYDSLCTSGVVRLHINSWLEVSFCLPHKIHYAAS
SLIPPEAIERSLKAIRPYHALLLLSDEKSLLGELPIDCSPALVRVIKTTSAVKNLQQLAQ
DADLALLQVFQLAAHLVYWGKAIIIYPLCENNVYMLSPNASVCLYSPLAEQFSHQFPSHD
LPSVLAKFSLPVSLSEFRNPLAPAVQETQLIQMVVWMLQRRLLIQLHTYVCLMASPSEEE
PRPREDDVPFTARVGGRSLSTPNALSFGSPTSSDDMTLTSPSMDNSSAELLPSGDSPLNQ
RMTENLLASLSEHERAAILSVPAAQNPEDLRMFARLLHYFRGRHHLEEIMYNENTRRSQL
LMLFDKFRSVLVVTTHEDPVIAVFQALLP

Sequence of entity 9 (D, K), FASTA

>7T3C_9 Ras-related GTP-binding protein A (chains D, K)
MPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNL
WDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDA
KIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECACFRTSIWDETLYKAWSSIVYQL
IPNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHYQCKEQRDVHRFEKISNIIKQFKL
SCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKL
ERVDGPKHSLLMR

Sequence of entity 10 (E), FASTA

>7T3C_10 Ras-related GTP-binding protein C (chains E)
MSLQYGAEETPLAGSYGAADSFPKDFGYGVEEEEEEAAAAGGGVGAGAGGGCGPGGADSS
KPRILLMGLRRSGKSSIQKVVFHKMSPNETLALESTNKIYKDDISNSSFVNFQIWDFPGQ
MDFFDPTFDYEMIFRGTGALIYVIDAQDDYMEALTRLHITVSKAYKVNPDMNFEVFIHKV
DGLSDDHKIETQRDIHQRANDDLADAGLEKLHLSFYLTSIYDHSIFEAFSKVVQKLIPQL
PTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDVSCIYG
LKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYNFHCFR
KAIHEVFEVGVTSHRSCGHQTSASSLKALTHNGTPRNAI

Sequence of entity 11 (L), FASTA

>7T3C_11 Ras-related GTP-binding protein C (chains L)
MSLQYGAEETPLAGSYGAADSFPKDFGYGVEEEEEEAAAAGGGVGAGAGGGCGPGGADSS
KPRILLMGLRRSGKNSIQKVVFHKMSPNETLFLESTNKIYKDDISNSSFVNFQIWDFPGQ
MDFFDPTFDYEMIFRGTGALIYVIDAQDDYMEALTRLHITVSKAYKVNPDMNFEVFIHKV
DGLSDDHKIETQRDIHQRANDDLADAGLEKLHLSFYLTSIYDHSIFEAFSKVVQKLIPQL
PTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDVSCIYG
LKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYNFHCFR
KAIHEVFEVGVTSHRSCGHQTSASSLKALTHNGTPRNAI

Ligands and cofactors

ID	Name	Formula	Copies
AF3	Aluminum fluoride	Al F3	3
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	3

Primary citation

Cryo-EM structures of the human GATOR1-Rag-Ragulator complex reveal a spatial-constraint regulated GAP mechanism. Egri, S.B., Ouch, C., Chou, H.T. et al. Mol Cell (2022) 82:1836. DOI 10.1016/j.molcel.2022.03.002 · PubMed

Other PDB entries of the same protein (UniProt Q8WTW4 (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
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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