7T3B: GATOR1-RAG-RAGULATOR - GAP Complex

GATOR1-RAG-RAGULATOR - GAP Complex. Determined by electron microscopy at 3.9 Å resolution. Released 6 Apr 2022.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Homo sapiens
Chains: 10
Atoms: 23,294
Mol. weight: 435.94 kDa
Ligands: AF3, GDP
Released: 6 Apr 2022

Explore 7T3B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7T3B contains 129 α-helices and 132 β-strands across 10 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: 42 helices, 56 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	11
β-strand	8-12	5	12
β-strand	23-25	3	12
β-strand	38-42	5	13
β-strand	51-54	4	13
β-strand	58	1	12
β-strand	66-70	5	12
α-helix	71-76	6
β-strand	85	1	11
β-strand	86-90	5	13
α-helix	92-94	3
β-strand	96	1	14
β-strand	99-104	6	15
α-helix	111-119	9
β-strand	125-127	3	14
β-strand	131-134	4	15
β-strand	137-145	9	15
β-strand	150	1	15
β-strand	153-155	3	14
β-strand	161-166	6	15
β-strand	170-176	7	16
α-helix	177	1
β-strand	184	1	17
α-helix	186-188	3
β-strand	190	1	17
α-helix	191-194	4
α-helix	195-200	6
α-helix	201-210	10
β-strand	216-225	10	16
α-helix	230-232	3
β-strand	239	1	16
β-strand	251-257	7	16
α-helix	267-269	3
α-helix	270-280	11
α-helix	282-285	4
α-helix	307-318	12
β-strand	331-337	7	16
α-helix	347-357	11
β-strand	364-367	4	16
β-strand	380-381	2	18
β-strand	397-398	2	18
β-strand	404	1	16
β-strand	407	1	16
α-helix	744-748	5
α-helix	750	1
β-strand	751	1	15
α-helix	752-754	3
β-strand	756	1	19
α-helix	763-769	7
β-strand	770	1	20
β-strand	773-777	5	19
α-helix	779-783	5
α-helix	795-808	14
β-strand	812-813	2	19
β-strand	851-856	6	19
β-strand	859-866	8	19
β-strand	869-875	7	19
β-strand	877	1	20
β-strand	886-893	8	16
β-strand	902-908	7	16
α-helix	913-915	3
α-helix	918-926	9
α-helix	937-939	3
β-strand	942-950	9	21
α-helix	953-960	8
α-helix	973-975	3
α-helix	978-993	16
α-helix	1178-1184	7
α-helix	1193-1195	3
α-helix	1201	1
β-strand	1204-1206	3	22
α-helix	1207-1217	11
α-helix	1224-1236	13
β-strand	1240-1242	3	22
α-helix	1250-1251	2
β-strand	1254-1255	2	23
β-strand	1257-1260	4	22
β-strand	1296-1297	2	23
α-helix	1298-1299	2
α-helix	1310-1312	3
β-strand	1351-1357	7	21
β-strand	1369-1375	7	21
β-strand	1382	1	24
β-strand	1384-1390	7	21
α-helix	1395-1411	17
β-strand	1414-1419	6	21
β-strand	1439-1442	4	24
α-helix	1446-1448	3
α-helix	1462-1464	3
α-helix	1465-1479	15
β-strand	1482-1485	4	24
α-helix	1487-1489	3
β-strand	1501-1504	4	24
β-strand	1509-1512	4	24
β-strand	1545-1550	6	24
α-helix	1567-1580	14
α-helix	1586-1595	10
α-helix	1596-1598	3

Chain B: 22 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	4
β-strand	14	1	5
β-strand	22	1	5
β-strand	26	1	4
α-helix	36-39	4
α-helix	41-44	4
β-strand	55-58	4	4
β-strand	62-69	8	4
β-strand	83-90	8	4
α-helix	98-116	19
α-helix	123-137	15
β-strand	144-148	5	6
β-strand	154-158	5	6
α-helix	163-169	7
β-strand	174-177	4	7
α-helix	181-183	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	7
β-strand	245-247	3	8
α-helix	249-252	4
α-helix	253-256	4
α-helix	259-268	10
β-strand	269	1	9
α-helix	270	1
α-helix	274-277	4
α-helix	278-286	9
α-helix	294-300	7
α-helix	303-305	3
β-strand	308	1	9
α-helix	310-319	10
β-strand	323-325	3	8
β-strand	328-329	2	10
α-helix	351-358	8
α-helix	362-369	8
α-helix	376-377	2
β-strand	378-379	2	10

Chain C: 23 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	9-16	8	27
β-strand	20-26	7	27
α-helix	66-73	8
β-strand	84-88	5	27
β-strand	91-99	9	27
β-strand	121-131	11	27
α-helix	136-160	25
α-helix	162-173	12
α-helix	194-197	4
α-helix	200-212	13
α-helix	222-225	4
β-strand	260-263	4	28
α-helix	267-273	7
α-helix	280-288	9
β-strand	294	1	28
α-helix	295-301	7
α-helix	306-318	13
β-strand	322-325	4	28
α-helix	326-328	3
β-strand	333-336	4	29
α-helix	337	1
α-helix	347-355	9
α-helix	361-367	7
β-strand	372-373	2	29
α-helix	384-399	16
β-strand	403-405	3	29
β-strand	406-412	7	30
α-helix	481-487	7
α-helix	492-500	9
α-helix	502-505	4
α-helix	507-515	9
β-strand	525	1	30
α-helix	526-533	8
α-helix	538-540	3
α-helix	541-546	6
β-strand	551-557	7	30
α-helix	561-563	3

Chain D: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	31
α-helix	20-27	8
α-helix	35-37	3
β-strand	47-52	6	31
β-strand	56-61	6	31
α-helix	67-75	9
α-helix	78-81	4
β-strand	87-88	2	31
β-strand	91-93	3	32
α-helix	99-114	16
β-strand	121-122	2	31
β-strand	123	1	33
β-strand	125-127	3	32
α-helix	134-150	17
β-strand	158	1	33
β-strand	161-162	2	32
α-helix	168-180	13
α-helix	184-197	14
β-strand	202-207	6	3
β-strand	213-218	6	3
α-helix	227-242	16
α-helix	243-245	3
β-strand	249-255	7	3
β-strand	260-265	6	3
β-strand	270-276	7	3
α-helix	283-297	15

Chain E: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	74-82	9
α-helix	87-90	4
β-strand	100-102	3	1
β-strand	114-116	3	1
α-helix	131-135	5
β-strand	139-144	6	2
α-helix	151-167	17
β-strand	172-177	6	2
α-helix	185-205	21
β-strand	214-215	2	2
α-helix	224-234	11
α-helix	240-251	12
β-strand	258-262	5	3
α-helix	276-277	2
α-helix	279-298	20
β-strand	315-320	6	3
β-strand	325-329	5	3
β-strand	336-341	6	3
α-helix	346-348	3
α-helix	349-366	18

Chain F: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	50-64	15
α-helix	65-67	3
α-helix	80-97	18
α-helix	115-119	5
α-helix	126-143	18
α-helix	148-150	3

Chain G: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-14	11
β-strand	19-25	7	25
β-strand	31-36	6	25
α-helix	47-62	16
β-strand	69-75	7	25
β-strand	80-86	7	25
β-strand	89-95	7	25
α-helix	101-124	24

Chain H: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-11	8
β-strand	19-25	7	25
β-strand	31-36	6	25
α-helix	42-45	4
α-helix	47-50	4
α-helix	52-61	10
β-strand	70-75	6	25
β-strand	78-85	8	25
β-strand	88-95	8	25
α-helix	100-109	10
α-helix	111-118	8

2 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
Ras-related GTP-binding protein C	E	protein	399	Homo sapiens	Q9HB90 (AlphaFold model)
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	protein	124	Homo sapiens	Q9UHA4 (AlphaFold model)
Ragulator complex protein LAMTOR2	G	protein	125	Homo sapiens	Q9Y2Q5
Ragulator complex protein LAMTOR5	J	protein	91	Homo sapiens	O43504
Ragulator complex protein LAMTOR4	I	protein	99	Homo sapiens	Q0VGL1
Ragulator complex protein LAMTOR1	F	protein	161	Homo sapiens	Q6IAA8
GATOR complex protein NPRL3	C	protein	569	Homo sapiens	Q12980
Ras-related GTP-binding protein A	D	protein	313	Homo sapiens	Q7L523

Sequence of entity 1 (E), FASTA

>7T3B_1 Ras-related GTP-binding protein C (chains E)
MSLQYGAEETPLAGSYGAADSFPKDFGYGVEEEEEEAAAAGGGVGAGAGGGCGPGGADSS
KPRILLMGLRRSGKSSIQKVVFHKMSPNETLALESTNKIYKDDISNSSFVNFQIWDFPGQ
MDFFDPTFDYEMIFRGTGALIYVIDAQDDYMEALTRLHITVSKAYKVNPDMNFEVFIHKV
DGLSDDHKIETQRDIHQRANDDLADAGLEKLHLSFYLTSIYDHSIFEAFSKVVQKLIPQL
PTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDVSCIYG
LKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYNFHCFR
KAIHEVFEVGVTSHRSCGHQTSASSLKALTHNGTPRNAI

Sequence of entity 2 (B), FASTA

>7T3B_2 GATOR complex protein NPRL2 (chains B)
MGSGCRIECIFFSEFHPTLGPKITYQVPEDFISRELFDTVQVYIITKPELQNKLITVTAM
EKKLIGCPVCIEHKKYSRNALLFNLGFVCDAQAKTCALEPIVKKLAGYLTTLELESSFVS
MEESKQKLVPIMTILLEELNASGRCTLPIDESNTIHLKVIEQRPDPPVAQEYDVPVFTKD
KEDFFNSQWDLTTQQILPYIDGFRHIQKISAEADVELNLVRIAIQNLLYYGVVTLVSILQ
YSNVYCPTPKVQDLVDDKSLQEACLSYVTKQGHKRASLRDVFQLYCSLSPGTTVRDLIGR
HPQQLQHVDERKLIQFGLMKNLIRRLQKYPVRVTREEQSHPARLYTGCHSYDEICCKTGM
SYHELDERLENDPNIIICWK

Sequence of entity 3 (A), FASTA

>7T3B_3 GATOR complex protein DEPDC5 (chains A)
MRTTKVYKLVIHKKGFGGSDDELVVNPKVFPHIKLGDIVEIAHPNDEYSPLLLQVKSLKE
DLQKETISVDQTVTQVFRLRPYQDVYVNVVDPKDVTLDLVELTFKDQYIGRGDMWRLKKS
LVSTCAYITQKVEFAGIRAQAGELWVKNEKVMCGYISEDTRVVFRSTSAMVYIFIQMSCE
MWDFDIYGDLYFEKAVNGFLADLFTKWKEKNCSHEVTVVLFSRTFYDAKSVDEFPEINRA
SIRQDHKGRFYEDFYKVVVQNERREEWTSLLVTIKKLFIQYPVLVRLEQAEGFPQGDNST
SAQGNYLEAINLSFNVFDKHYINRNFDRTGQMSVVITPGVGVFEVDRLLMILTKQRMIDN
GIGVDLVCMGEQPLHAVPLFKLHNRSAPRDSRLGDDYNIPHWINHSFYTSKSQLFCNSFT
PRIKLAGKKPASEKAKNGRDTSLGSPKESENALPIQVDYDAYDAQVFRLPGPSRAQCLTT
CRSVRERESHSRKSASSCDVSSSPSLPSRTLPTEEVRSQASDDSSLGKSANILMIPHPHL
HQYEVSSSLGYTSTRDVLENMMEPPQRDSSAPGRFHVGSAESMLHVRPGGYTPQRALINP
FAPSRMPMKLTSNRRRWMHTFPVGPSGEAIQIHHQTRQNMAELQGSGQRDPTHSSAELLE
LAYHEAAGRHSNSRQPGDGMSFLNFSGTEELSVGLLSNSGAGMNPRTQNKDSLEDSVSTS
PDPILTLSAPPVVPGFCCTVGVDWKSLTTPACLPLTTDYFPDRQGLQNDYTEGCADLLPE
ADIDRRDEDGVQMTAQQVFEEFICQRLMQGYQIIVQPKTQKPNPAVPPPLSSSPLYSRGL
VSRNRPEEEDQYWLSMGRTFHKVTLKDKMITVTRYLPKYPYESAQIHYTYSLCPSHSDSE
FVSCWVEFSHERLEEYKWNYLDQYICSAGSEDFSLIESLKFWRTRFLLLPACVTATKRIT
EGEAHCDIYGDRPRADEDEWQLLDGFVRFVEGLNRIRRRHRSDRMMRKGTAMKGLQMTGP
ISTHSLESTAPPVGKKGTSALSALLEMEASQKCLGEQQAAVHGGKSSAQSAESSSVAMTP
TYMDSPRKDGAFFMEFVRSPRTASSAFYPQVSVDQTATPMLDGTSLGICTGQSMDRGNSQ
TFGNSQNIGEQGYSSTNSSDSSSQQLVASSLTSSSTLTEILEAMKHPSTGVQLLSEQKGL
SPYCFISAEVVHWLVNHVEGIQTQAMAIDIMQKMLEEQLITHASGEAWRTFIYGFYFYKI
VTDKEPDRVAMQQPATTWHTAGVDDFASFQRKWFEVAFVAEELVHSEIPAFLLPWLPSRP
ASYASRHSSFSRSFGGRSQAAALLAATVPEQRTVTLDVDVNNRTDRLEWCSCYYHGNFSL
NAAFEIKLHWMAVTAAVLFEMVQGWHRKATSCGFLLVPVLEGPFALPSYLYGDPLRAQLF
IPLNISCLLKEGSEHLFDSFEPETYWDRMHLFQEAIAHRFGFVQDKYSASAFNFPAENKP
QYIHVTGTVFLQLPYSKRKFSGQQRRRRNSTSSTNQNMFCEERVGYNWAYNTMLTKTWRS
SATGDEKFADRLLKDFTDFCINRDNRLVTFWTSCLEKMHASAP

Sequence of entity 4 (H), FASTA

>7T3B_4 Ragulator complex protein LAMTOR3 (chains H)
MADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQG
SKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQV
VEVS

Sequence of entity 5 (G), FASTA

>7T3B_5 Ragulator complex protein LAMTOR2 (chains G)
MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNG
NQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLT
QVAAS

Sequence of entity 6 (J), FASTA

>7T3B_6 Ragulator complex protein LAMTOR5 (chains J)
MEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPT
DIPVVCLESDNGNIMIQKHDGITVAVHKMAS

Sequence of entity 7 (I), FASTA

>7T3B_7 Ragulator complex protein LAMTOR4 (chains I)
MTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMN
VPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV

Sequence of entity 8 (F), FASTA

>7T3B_8 Ragulator complex protein LAMTOR1 (chains F)
MGCCYSSENEDSDQDREERKLLLDPSSPPTKALNGAEPNYHSLPSARTDEQALLSSILAK
TASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLA
SEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGIP

Sequence of entity 9 (C), FASTA

>7T3B_9 GATOR complex protein NPRL3 (chains C)
MRDNTSPISVILVSSGSRGNKLLFRYPFQRSQEHPASQTSKPRSRYAASNTGDHADEQDG
DSRFSDVILATILATKSEMCGQKFELKIDNVRFVGHPTLLQHALGQISKTDPSPKREAPT
MILFNVVFALRANADPSVINCLHNLSRRIATVLQHEERRCQYLTREAKLILALQDEVSAM
ADGNEGPQSPFHHILPKCKLARDLKEAYDSLCTSGVVRLHINSWLEVSFCLPHKIHYAAS
SLIPPEAIERSLKAIRPYHALLLLSDEKSLLGELPIDCSPALVRVIKTTSAVKNLQQLAQ
DADLALLQVFQLAAHLVYWGKAIIIYPLCENNVYMLSPNASVCLYSPLAEQFSHQFPSHD
LPSVLAKFSLPVSLSEFRNPLAPAVQETQLIQMVVWMLQRRLLIQLHTYVCLMASPSEEE
PRPREDDVPFTARVGGRSLSTPNALSFGSPTSSDDMTLTSPSMDNSSAELLPSGDSPLNQ
RMTENLLASLSEHERAAILSVPAAQNPEDLRMFARLLHYFRGRHHLEEIMYNENTRRSQL
LMLFDKFRSVLVVTTHEDPVIAVFQALLP

Sequence of entity 10 (D), FASTA

>7T3B_10 Ras-related GTP-binding protein A (chains D)
MPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNL
WDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDA
KIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECACFRTSIWDETLYKAWSSIVYQL
IPNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHYQCKEQRDVHRFEKISNIIKQFKL
SCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKL
ERVDGPKHSLLMR

Ligands and cofactors

ID	Name	Formula	Copies
AF3	Aluminum fluoride	Al F3	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

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 Q9HB90 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3LLU 1.4 Å, Crystal structure of the nucleotide-binding domain of Ras-related GTP-binding protein C
6S6D 2.5 Å, Crystal structure of RagA-Q66L-GTP/RagC-S75N-GDP GTPase heterodimer complex
6S6A 2.63 Å, Crystal structure of RagA-Q66L/RagC-T90N GTPase heterodimer complex
6EHR 2.9 Å, The crystal structure of the human LAMTOR-RagA CTD-RagC CTD complex
7UX2 2.9 Å, cryo-EM structure of the Raptor-TFEB-Rag-Ragulator complex
6U62 3.18 Å, Raptor-Rag-Ragulator complex
6WJ2 3.2 Å, CryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in the pre-GAP state
7UXC 3.2 Å, cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex with symmetry expansion
7UXH 3.2 Å, cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex
9ED4 3.23 Å, A composite map of mTORC1-Rag-Ragultor-4EBP1 on membrane
6ULG 3.31 Å, Cryo-EM structure of the FLCN-FNIP2-Rag-Ragulator complex
8DHB 3.53 Å, Active FLCN GAP complex

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