7T3A: GATOR1-RAG-RAGULATOR - Inhibitory Complex

GATOR1-RAG-RAGULATOR - Inhibitory 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: 10
Atoms: 23,310
Mol. weight: 435.6 kDa
Ligands: GNP
Released: 6 Apr 2022

Explore 7T3A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7T3A contains 119 α-helices and 136 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: 40 helices, 61 β-strands

Element	Residues	Length	Sheet
β-strand	7-12	6	1
β-strand	16	1	2
β-strand	19	1	2
β-strand	23-25	3	1
β-strand	38-42	5	3
β-strand	51-54	4	3
β-strand	57-58	2	1
β-strand	66-70	5	1
α-helix	71-77	7
α-helix	79-80	2
β-strand	84-85	2	1
β-strand	86-89	4	3
α-helix	93-95	3
β-strand	96	1	4
β-strand	99-104	6	5
α-helix	111-119	9
β-strand	125-126	2	4
β-strand	131-134	4	5
β-strand	137-144	8	5
β-strand	151	1	5
β-strand	154-155	2	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	195-199	5
α-helix	200-209	10
β-strand	215	1	6
β-strand	218-222	5	6
β-strand	225	1	8
β-strand	226	1	9
β-strand	239	1	8
β-strand	251	1	8
β-strand	254-258	5	6
α-helix	267-269	3
α-helix	270-280	11
α-helix	282-284	3
β-strand	294	1	9
α-helix	307-317	11
β-strand	331-337	7	6
β-strand	345	1	10
α-helix	347-359	13
β-strand	363-367	5	6
β-strand	380-382	3	10
β-strand	396-398	3	10
β-strand	404	1	6
β-strand	407	1	6
α-helix	745-748	4
α-helix	750	1
β-strand	751	1	5
α-helix	752-754	3
β-strand	756	1	11
α-helix	759-762	4
α-helix	763-768	6
β-strand	770-777	8	11
α-helix	779-782	4
α-helix	795-808	14
β-strand	812-813	2	11
β-strand	851-856	6	11
β-strand	859-866	8	11
β-strand	869-877	9	11
β-strand	886-893	8	6
β-strand	902-908	7	6
α-helix	918-927	10
α-helix	937-939	3
β-strand	942-950	9	12
α-helix	953-960	8
α-helix	976-993	18
α-helix	1178-1185	8
α-helix	1193-1195	3
α-helix	1200-1201	2
β-strand	1204-1206	3	13
α-helix	1207-1217	11
α-helix	1224-1236	13
β-strand	1240-1242	3	13
β-strand	1254-1255	2	14
β-strand	1257-1260	4	13
α-helix	1287-1290	4
β-strand	1296-1298	3	14
α-helix	1302-1304	3
α-helix	1310-1312	3
β-strand	1351-1357	7	12
β-strand	1369-1375	7	12
β-strand	1377-1378	2	14
β-strand	1384-1390	7	12
α-helix	1395-1410	16
β-strand	1414-1419	6	12
β-strand	1439-1442	4	15
α-helix	1446-1448	3
α-helix	1462-1464	3
α-helix	1465-1479	15
β-strand	1482-1485	4	15
β-strand	1501-1504	4	15
β-strand	1509-1512	4	15
β-strand	1545-1550	6	15
α-helix	1568-1580	13
α-helix	1583-1585	3
α-helix	1586-1595	10
α-helix	1596-1598	3

Chain B: 15 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	16
β-strand	22-26	5	16
β-strand	55	1	17
β-strand	58-59	2	16
β-strand	62-65	4	16
β-strand	66	1	17
β-strand	69	1	18
β-strand	83	1	18
β-strand	84-90	7	16
α-helix	98-116	19
α-helix	124-139	16
β-strand	145-148	4	19
β-strand	154-157	4	19
α-helix	165-168	4
β-strand	174-177	4	20
α-helix	181-183	3
α-helix	191-196	6
α-helix	207-210	4
α-helix	217-228	12
β-strand	232-235	4	20
β-strand	245-247	3	21
α-helix	253-256	4
α-helix	259-267	9
β-strand	269	1	22
α-helix	274-277	4
α-helix	278-286	9
α-helix	294-300	7
β-strand	308	1	22
α-helix	310-317	8
β-strand	323-325	3	21
β-strand	328-329	2	23
α-helix	351-358	8
α-helix	362-369	8
β-strand	378-379	2	23

Chain C: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	9-16	8	24
β-strand	22-26	5	24
α-helix	66-72	7
α-helix	77-79	3
β-strand	84-86	3	24
β-strand	92-95	4	24
β-strand	99	1	24
β-strand	121-130	10	24
α-helix	136-159	24
α-helix	162-173	12
α-helix	200-211	12
β-strand	260-263	4	25
α-helix	267-273	7
α-helix	280-287	8
α-helix	295-301	7
α-helix	306-319	14
β-strand	322-325	4	25
β-strand	333-336	4	26
α-helix	348-355	8
α-helix	361-367	7
β-strand	372-373	2	26
α-helix	384-399	16
β-strand	403-405	3	26
β-strand	406-412	7	27
α-helix	481-488	8
α-helix	492-499	8
α-helix	507-515	9
α-helix	517-519	3
β-strand	521	1	27
α-helix	526-533	8
α-helix	537-546	10
β-strand	551-557	7	27
α-helix	559-563	5

Chain K: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	8-13	6	28
α-helix	20-27	8
α-helix	35-38	4
β-strand	45-52	8	28
β-strand	56-63	8	28
α-helix	67-75	9
α-helix	78-82	5
β-strand	87-91	5	28
α-helix	99-116	18
β-strand	121-126	6	28
α-helix	129-131	3
α-helix	134-151	18
β-strand	158-161	4	28
α-helix	168-180	13
α-helix	184-198	15
β-strand	202-207	6	29
β-strand	213-218	6	29
α-helix	228-242	15
α-helix	243-245	3
β-strand	251-256	6	29
β-strand	259-265	7	29
β-strand	270-275	6	29
α-helix	284-296	13

Chain L: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	64-65	2	30
α-helix	74-85	12
α-helix	102-110	9
α-helix	126-129	4
β-strand	139-144	6	30
α-helix	150-160	11
α-helix	162-167	6
β-strand	173-177	5	30
α-helix	185-198	14
α-helix	200-203	4
β-strand	213	1	30
α-helix	225-234	10
α-helix	240-250	11
β-strand	258-262	5	29
α-helix	281-299	19
β-strand	316-318	3	29
β-strand	324-330	7	29
β-strand	336-342	7	29
α-helix	351-357	7

Chain M: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	48-63	16
α-helix	79-94	16
α-helix	108-110	3
α-helix	115-119	5
α-helix	122-125	4
α-helix	126-141	16
β-strand	155	1	31

Chain N: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	31
α-helix	4-11	8
β-strand	21-25	5	32
β-strand	31-36	6	32
α-helix	44-46	3
α-helix	47-58	12
β-strand	71-73	3	32
β-strand	80-86	7	32
β-strand	89-95	7	32
α-helix	101-115	15
α-helix	118-123	6

Chain O: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-11	8
α-helix	13-15	3
β-strand	19-26	8	32
β-strand	31-35	5	32
α-helix	42-44	3
α-helix	47-59	13
β-strand	70-74	5	32
β-strand	78-85	8	32
β-strand	88-95	8	32
α-helix	100-109	10
α-helix	111-113	3
α-helix	115-119	5

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
GATOR complex protein DEPDC5	A	protein	1603	Homo sapiens	O75140 (AlphaFold model)
GATOR complex protein NPRL2	B	protein	380	Homo sapiens	Q8WTW4 (AlphaFold model)
GATOR complex protein NPRL3	C	protein	569	Homo sapiens	Q12980 (AlphaFold model)
Ras-related GTP-binding protein A	K	protein	313	Homo sapiens	Q7L523 (AlphaFold model)
Ras-related GTP-binding protein C	L	protein	399	Homo sapiens	Q9HB90
Ragulator complex protein LAMTOR1	M	protein	161	Homo sapiens	Q6IAA8
Ragulator complex protein LAMTOR2	N	protein	125	Homo sapiens	Q9Y2Q5
Ragulator complex protein LAMTOR3	O	protein	124	Homo sapiens	Q9UHA4
Ragulator complex protein LAMTOR4	P	protein	99	Homo sapiens	Q0VGL1
Ragulator complex protein LAMTOR5	Q	protein	91	Homo sapiens	O43504

Sequence of entity 1 (A), FASTA

>7T3A_1 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 2 (B), FASTA

>7T3A_2 GATOR complex protein NPRL2 (chains B)
MGSGCRIECIFFSEFHPTLGPKITYQVPEDFISRELFDTVQVYIITKPELQNKLITVTAM
EKKLIGCPVCIEHKKYSRNALLFNLGFVCDAQAKTCALEPIVKKLAGYLTTLELESSFVS
MEESKQKLVPIMTILLEELNASGRCTLPIDESNTIHLKVIEQRPDPPVAQEYDVPVFTKD
KEDFFNSQWDLTTQQILPYIDGFRHIQKISAEADVELNLVRIAIQNLLYYGVVTLVSILQ
YSNVYCPTPKVQDLVDDKSLQEACLSYVTKQGHKRASLRDVFQLYCSLSPGTTVRDLIGR
HPQQLQHVDERKLIQFGLMKNLIRRLQKYPVRVTREEQSHPARLYTGCHSYDEICCKTGM
SYHELDERLENDPNIIICWK

Sequence of entity 3 (C), FASTA

>7T3A_3 GATOR complex protein NPRL3 (chains C)
MRDNTSPISVILVSSGSRGNKLLFRYPFQRSQEHPASQTSKPRSRYAASNTGDHADEQDG
DSRFSDVILATILATKSEMCGQKFELKIDNVRFVGHPTLLQHALGQISKTDPSPKREAPT
MILFNVVFALRANADPSVINCLHNLSRRIATVLQHEERRCQYLTREAKLILALQDEVSAM
ADGNEGPQSPFHHILPKCKLARDLKEAYDSLCTSGVVRLHINSWLEVSFCLPHKIHYAAS
SLIPPEAIERSLKAIRPYHALLLLSDEKSLLGELPIDCSPALVRVIKTTSAVKNLQQLAQ
DADLALLQVFQLAAHLVYWGKAIIIYPLCENNVYMLSPNASVCLYSPLAEQFSHQFPSHD
LPSVLAKFSLPVSLSEFRNPLAPAVQETQLIQMVVWMLQRRLLIQLHTYVCLMASPSEEE
PRPREDDVPFTARVGGRSLSTPNALSFGSPTSSDDMTLTSPSMDNSSAELLPSGDSPLNQ
RMTENLLASLSEHERAAILSVPAAQNPEDLRMFARLLHYFRGRHHLEEIMYNENTRRSQL
LMLFDKFRSVLVVTTHEDPVIAVFQALLP

Sequence of entity 4 (K), FASTA

>7T3A_4 Ras-related GTP-binding protein A (chains K)
MPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNL
WDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDA
KIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECACFRTSIWDETLYKAWSSIVYQL
IPNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHYQCKEQRDVHRFEKISNIIKQFKL
SCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKL
ERVDGPKHSLLMR

Sequence of entity 5 (L), FASTA

>7T3A_5 Ras-related GTP-binding protein C (chains L)
MSLQYGAEETPLAGSYGAADSFPKDFGYGVEEEEEEAAAAGGGVGAGAGGGCGPGGADSS
KPRILLMGLRRSGKNSIQKVVFHKMSPNETLFLESTNKIYKDDISNSSFVNFQIWDFPGQ
MDFFDPTFDYEMIFRGTGALIYVIDAQDDYMEALTRLHITVSKAYKVNPDMNFEVFIHKV
DGLSDDHKIETQRDIHQRANDDLADAGLEKLHLSFYLTSIYDHSIFEAFSKVVQKLIPQL
PTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDVSCIYG
LKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYNFHCFR
KAIHEVFEVGVTSHRSCGHQTSASSLKALTHNGTPRNAI

Sequence of entity 6 (M), FASTA

>7T3A_6 Ragulator complex protein LAMTOR1 (chains M)
MGCCYSSENEDSDQDREERKLLLDPSSPPTKALNGAEPNYHSLPSARTDEQALLSSILAK
TASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLA
SEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGIP

Sequence of entity 7 (N), FASTA

>7T3A_7 Ragulator complex protein LAMTOR2 (chains N)
MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNG
NQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLT
QVAAS

Sequence of entity 8 (O), FASTA

>7T3A_8 Ragulator complex protein LAMTOR3 (chains O)
MADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQG
SKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQV
VEVS

Sequence of entity 9 (P), FASTA

>7T3A_9 Ragulator complex protein LAMTOR4 (chains P)
MTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMN
VPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV

Sequence of entity 10 (Q), FASTA

>7T3A_10 Ragulator complex protein LAMTOR5 (chains Q)
MEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPT
DIPVVCLESDNGNIMIQKHDGITVAVHKMAS

Ligands and cofactors

ID	Name	Formula	Copies
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	1

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 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
9XZY 3.8 Å, DEPDC5 dimer (tandem DEPDC5) focused map
7T3B 3.9 Å, GATOR1-RAG-RAGULATOR - GAP Complex
6CES 4.0 Å, Cryo-EM structure of GATOR1-RAG
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

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