8FW5: Chimeric HsGATOR1-SpGtr-SpLam complex

Chimeric HsGATOR1-SpGtr-SpLam complex. Determined by electron microscopy at 3.08 Å resolution. Released 26 Jul 2023.

Method: Electron microscopy
Resolution: 3.08 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 9
Atoms: 22,853
Mol. weight: 451.15 kDa
Ligands: MG, AF3, GDP
Released: 26 Jul 2023

Explore 8FW5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FW5 contains 122 α-helices and 128 β-strands across 9 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: 38 helices, 56 β-strands

Element	Residues	Length	Sheet
β-strand	7-12	6	1
β-strand	16	1	2
β-strand	19	1	2
β-strand	23-24	2	1
β-strand	25	1	3
β-strand	38-42	5	4
β-strand	51-54	4	4
β-strand	58	1	3
β-strand	66-70	5	1
α-helix	71-76	6
β-strand	84-85	2	1
β-strand	86-90	5	4
β-strand	96	1	5
β-strand	99-104	6	6
α-helix	111-120	10
β-strand	125	1	5
β-strand	131-134	4	6
β-strand	137-145	9	6
β-strand	150-151	2	6
β-strand	155	1	5
β-strand	161-166	6	6
β-strand	169-176	8	7
α-helix	179-182	4
α-helix	191-194	4
α-helix	195-200	6
α-helix	201-210	10
β-strand	217-226	10	7
β-strand	242-244	3	7
β-strand	250-259	10	7
α-helix	267-269	3
α-helix	270-279	10
α-helix	281-284	4
β-strand	297-298	2	7
α-helix	299-300	2
α-helix	306-318	13
β-strand	330-337	8	7
β-strand	342-344	3	8
α-helix	347-359	13
β-strand	363-367	5	7
β-strand	379-381	3	8
β-strand	397-398	2	8
β-strand	406-407	2	7
α-helix	416-418	3
α-helix	629-638	10
α-helix	659-669	11
α-helix	732-734	3
α-helix	739-740	2
α-helix	744-748	5
β-strand	751	1	6
β-strand	756-757	2	9
α-helix	763-768	6
β-strand	770-777	8	9
α-helix	795-809	15
β-strand	812-814	3	9
β-strand	851-856	6	9
β-strand	859-865	7	9
β-strand	870-877	8	9
β-strand	886-893	8	7
α-helix	901	1
β-strand	902-908	7	7
α-helix	918-926	9
α-helix	932-935	4
α-helix	937-939	3
β-strand	942-950	9	10
α-helix	953-961	9
α-helix	979-993	15
α-helix	1178-1184	7
β-strand	1204-1206	3	11
α-helix	1207-1216	10
α-helix	1224-1236	13
β-strand	1240-1242	3	11
α-helix	1249-1251	3
β-strand	1254-1255	2	12
β-strand	1257-1260	4	11
β-strand	1296-1298	3	12
α-helix	1301-1303	3
β-strand	1351-1357	7	10
β-strand	1369-1375	7	10
β-strand	1377-1378	2	12
β-strand	1382	1	13
α-helix	1383	1
β-strand	1384-1390	7	10
α-helix	1395-1411	17
β-strand	1414-1419	6	10
β-strand	1439-1442	4	13
α-helix	1465-1479	15
β-strand	1482-1485	4	13
α-helix	1487-1489	3
β-strand	1501-1504	4	13
β-strand	1509-1512	4	13
β-strand	1545-1550	6	13
α-helix	1568-1580	13
α-helix	1583-1585	3
α-helix	1586-1595	10

Chain B: 21 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	14
β-strand	21-26	6	14
α-helix	34-39	6
β-strand	56-58	3	14
β-strand	62-65	4	14
β-strand	69	1	14
β-strand	83-90	8	14
α-helix	99-116	18
α-helix	122-125	4
α-helix	128-140	13
β-strand	144-148	5	15
β-strand	154-158	5	15
α-helix	163-170	8
β-strand	174-177	4	16
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	217-229	13
β-strand	233-236	4	16
β-strand	244-247	4	17
α-helix	249-251	3
α-helix	252-255	4
α-helix	258-267	10
β-strand	269	1	18
α-helix	270	1
α-helix	274-277	4
α-helix	278-286	9
α-helix	294-300	7
β-strand	308	1	18
α-helix	310-319	10
β-strand	323-326	4	17
β-strand	328-329	2	19
α-helix	351-357	7
α-helix	362-369	8
β-strand	378-379	2	19

Chain C: 21 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	9-16	8	14
β-strand	21-25	5	14
α-helix	66-73	8
α-helix	77-79	3
β-strand	84-87	4	14
β-strand	91-95	5	14
β-strand	98-99	2	14
β-strand	121-131	11	14
α-helix	136-160	25
α-helix	162-172	11
α-helix	194-197	4
α-helix	199-212	14
β-strand	260-263	4	20
α-helix	267-273	7
α-helix	280-288	9
β-strand	294	1	20
α-helix	295-301	7
α-helix	306-318	13
β-strand	322-325	4	20
α-helix	326-328	3
β-strand	333-336	4	21
α-helix	347-355	9
α-helix	361-367	7
β-strand	372-373	2	21
α-helix	374-377	4
α-helix	384-399	16
β-strand	403-405	3	21
β-strand	406-412	7	22
α-helix	481-487	7
α-helix	492-500	9
α-helix	502-505	4
α-helix	507-515	9
β-strand	525	1	22
α-helix	526-532	7
α-helix	537-546	10
β-strand	551-557	7	22

Chain D: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	23
α-helix	15-22	8
α-helix	29-33	5
α-helix	36-38	3
β-strand	40-46	7	23
β-strand	52-58	7	23
α-helix	62-68	7
α-helix	73-76	4
β-strand	82-88	7	23
α-helix	94-111	18
β-strand	116-122	7	23
α-helix	124-126	3
α-helix	129-131	3
α-helix	136-146	11
β-strand	151-156	6	23
α-helix	163-175	13
α-helix	179-192	14
β-strand	197-202	6	24
β-strand	208-213	6	24
α-helix	224-241	18
β-strand	246-252	7	24
β-strand	257-262	6	24
β-strand	267-273	7	24
α-helix	280-300	21

Chain E: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	25
α-helix	16-19	4
α-helix	20-24	5
β-strand	54-56	3	25
α-helix	70-75	6
β-strand	77-85	9	25
α-helix	91-107	17
β-strand	112-118	7	25
α-helix	125-146	22
β-strand	153-157	5	25
α-helix	164-176	13
α-helix	180-194	15
β-strand	198-203	6	24
β-strand	208-212	5	24
α-helix	219-239	21
α-helix	253-256	4
β-strand	258-263	6	24
β-strand	267-273	7	24
β-strand	278-285	8	24
α-helix	292-309	18

Chain F: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	43-59	17
α-helix	82-87	6
α-helix	95-97	3
β-strand	100-102	3	26
α-helix	103-105	3
α-helix	106-124	19

Chain G: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-12	9
β-strand	22-25	4	27
β-strand	31-34	4	27
α-helix	39-40	2
α-helix	43-67	25
α-helix	73-75	3
α-helix	81-85	5
β-strand	91	1	28
β-strand	93-98	6	27
β-strand	102-108	7	27
β-strand	123-128	6	27
α-helix	135-152	18
α-helix	153-155	3

Chain H: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2-9	8
β-strand	17-19	3	27
β-strand	22	1	29
α-helix	39-53	15
α-helix	54-56	3
β-strand	62-67	6	27
β-strand	69	1	28
β-strand	75-77	3	27
β-strand	80-81	2	29
β-strand	88-89	2	29
β-strand	92-94	3	27
α-helix	97-100	4
α-helix	104-116	13

1 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	401	Homo sapiens	Q8WTW4 (AlphaFold model)
GATOR complex protein NPRL3	C	protein	590	Homo sapiens	Q12980 (AlphaFold model)
GTP-binding protein Gtr1	D	protein	321	Escherichia coli	O74824 (AlphaFold model)
GTP-binding protein Gtr2	E	protein	314	Escherichia coli	O74544
Schizosaccharomyces pombe LAM1, Human LAMTOR1 ortholog	F	protein	377	Escherichia coli	C6Y4C6, P08515
Schizosaccharomyces pombe LAM2, Human LAMTOR2 ortholog	G	protein	181	Escherichia coli	Q9Y7J2
Schizosaccharomyces pombe LAM3, Human LAMTOR3 ortholog	H	protein	117	Escherichia coli	G2TRJ4
Schizosaccharomyces pombe LAM4, Human LAMTOR5 ortholog	I	protein	81	Escherichia coli	C6Y4A8

Sequence of entity 1 (A), FASTA

>8FW5_1 GATOR complex protein DEPDC5 (chains A)
MRTTKVYKLVIHKKGFGGSDDELVVNPKVFPHIKLGDIVEIAHPNDEYSPLLLQVKSLKE
DLQKETISVDQTVTQVFRLRPYQDVYVNVVDPKDVTLDLVELTFKDQYIGRGDMWRLKKS
LVSTCAYITQKVEFAGIRAQAGELWVKNEKVMCGYISEDTRVVFRSTSAMVYIFIQMSCE
MWDFDIYGDLYFEKAVNGFLADLFTKWKEKNCSHEVTVVLFSRTFYDAKSVDEFPEINRA
SIRQDHKGRFYEDFYKVVVQNERREEWTSLLVTIKKLFIQYPVLVRLEQAEGFPQGDNST
SAQGNYLEAINLSFNVFDKHYINRNFDRTGQMSVVITPGVGVFEVDRLLMILTKQRMIDN
GIGVDLVCMGEQPLHAVPLFKLHNRSAPRDSRLGDDYNIPHWINHSFYTSKSQLFCNSFT
PRIKLAGKKPASEKAKNGRDTSLGSPKESENALPIQVDYDAYDAQVFRLPGPSRAQCLTT
CRSVRERESHSRKSASSCDVSSSPSLPSRTLPTEEVRSQASDDSSLGKSANILMIPHPHL
HQYEVSSSLGYTSTRDVLENMMEPPQRDSSAPGRFHVGSAESMLHVRPGGYTPQRALINP
FAPSRMPMKLTSNRRRWMHTFPVGPSGEAIQIHHQTRQNMAELQGSGQRDPTHSSAELLE
LAYHEAAGRHSNSPQPGDGMSFLNFSGTEELSVGLLSNSGAGMNPRTQNKDSLEDSVSTS
PDPILTLSAPPVVPGFCCTVGVDWKSLTTPACLPLTTDYFPDRQGLQNDYTEGCADLLPE
ADIDRRDEDGVQMTAQQVFEEFICQRLMQGYQIIVQPKTQKPNPAVPPPLSSSPLYSRGL
VSRNRPEEEDQYWLSMGRTFHKVTLKDKMITVTRYLPKYPYESAQIHYTYSLCPSHSDSE
FVSCWVEFSHERLEEYKWNYLDQYICSAGSEDFSLIESLKFWRTRFLLLPACVTATKRIT
EGEAHCDIYGDRPRADEDEWQLLDGFVRFVEGLNRIRRRHRSDRMMRKGTAMKGLQMTGP
ISTHSLESTAPPVGKKGTSALSALLEMEASQKCLGEQQAAVHGGKSSAQSAESSSVAMTP
TYMDSPRKDGAFFMEFVRSPRTASSAFYPQVSVDQTATPMLDGTSLGICTGQSMDRGNSQ
TFGNSQNIGEQGYSSTNSSDSSSQQLVASSLTSSSTLTEILEAMKHPSTGVQLLSEQKGL
SPYCFISAEVVHWLVNHVEGIQTQAMAIDIMQKMLEEQLITHASGEAWRTFIYGFYFYKI
VTDKEPDRVAMQQPATTWHTAGVDDFASFQRKWFEVAFVAEELVHSEIPAFLLPWLPSRP
ASYASRHSSFSRSFGGRSQAAALLAATVPEQRTVTLDVDVNNRTDRLEWCSCYYHGNFSL
NAAFEIKLHWMAVTAAVLFEMVQGWHRKATSCGFLLVPVLEGPFALPSYLYGDPLRAQLF
IPLNISCLLKEGSEHLFDSFEPETYWDRMHLFQEAIAHRFGFVQDKYSASAFNFPAENKP
QYIHVTGTVFLQLPYSKRKFSGQQRRRRNSTSSTNQNMFCEERVGYNWAYNTMLTKTWRS
SATGDEKFADRLLKDFTDFCINRDNRLVTFWTSCLEKMHASAP

Sequence of entity 2 (B), FASTA

>8FW5_2 GATOR complex protein NPRL2 (chains B)
MGYPYDVPDYADLNGGGGGSTMGSGCRIECIFFSEFHPTLGPKITYQVPEDFISRELFDT
VQVYIITKPELQNKLITVTAMEKKLIGCPVCIEHKKYSRNALLFNLGFVCDAQAKTCALE
PIVKKLAGYLTTLELESSFVSMEESKQKLVPIMTILLEELNASGRCTLPIDESNTIHLKV
IEQRPDPPVAQEYDVPVFTKDKEDFFNSQWDLTTQQILPYIDGFRHIQKISAEADVELNL
VRIAIQNLLYYGVVTLVSILQYSNVYCPTPKVQDLVDDKSLQEACLSYVTKQGHKRASLR
DVFQLYCSLSPGTTVRDLIGRHPQQLQHVDERKLIQFGLMKNLIRRLQKYPVRVTREEQS
HPARLYTGCHSYDEICCKTGMSYHELDERLENDPNIIICWK

Sequence of entity 3 (C), FASTA

>8FW5_3 GATOR complex protein NPRL3 (chains C)
MGYPYDVPDYADLNGGGGGSTMRDNTSPISVILVSSGSRGNKLLFRYPFQRSQEHPASQT
SKPRSRYAASNTGDHADEQDGDSRFSDVILATILATKSEMCGQKFELKIDNVRFVGHPTL
LQHALGQISKTDPSPKREAPTMILFNVVFALRANADPSVINCLHNLSRRIATVLQHEERR
CQYLTREAKLILALQDEVSAMADGNEGPQSPFHHILPKCKLARDLKEAYDSLCTSGVVRL
HINSWLEVSFCLPHKIHYAASSLIPPEAIERSLKAIRPYHALLLLSDEKSLLGELPIDCS
PALVRVIKTTSAVKNLQQLAQDADLALLQVFQLAAHLVYWGKAIIIYPLCENNVYMLSPN
ASVCLYSPLAEQFSHQFPSHDLPSVLAKFSLPVSLSEFRNPLAPAVQETQLIQMVVWMLQ
RRLLIQLHTYVCLMASPSEEEPRPREDDVPFTARVGGRSLSTPNALSFGSPTSSDDMTLT
SPSMDNSSAELLPSGDSPLNQRMTENLLASLSEHERAAILSVPAAQNPEDLRMFARLLHY
FRGRHHLEEIMYNENTRRSQLLMLFDKFRSVLVVTTHEDPVIAVFQALLP

Sequence of entity 4 (D), FASTA

>8FW5_4 GTP-binding protein Gtr1 (chains D)
MRKKVLLMGRSGSGKSSMRSIVFSNYVAKDTRRLGATIDIEHSHVRFLGNLVLNLWDCGG
QEAFMENYLSAQRDHIFRNVQVLIYVFDVESREFERDLVTFRNCLEATVANSPQARVFCL
IHKMDLVQEDLRDLVFEERKAILLETSKDLETTCLATSIWDETLFKAWSAIVYTLIPNTP
TLESHLREFAKAAEAAEVILFERTTFLVISSYSSESNPATDAHRFEKISNIVKQFKLSCS
KMQAQFTTFELRGGNFSAFIVPYTEDTYILVVIADPEIESAVTLMNIQSARRFIEASKSA
SDGIQLQPGSGGSHHHHHHHH

Sequence of entity 5 (E), FASTA

>8FW5_5 GTP-binding protein Gtr2 (chains E)
MKPRKIILMGLRRSGKSSIQKVVFYKMPPNETLALESTSKLTQDHISSFIDFSVWDFPGQ
VDVFDAAFDFESIFTQVGALIFVIDAQDDYLDALARLHVTVARVVTINPNICIEVFIHKV
DGLSDEFKIDTQRDIQQRTQDELADIGLENVPISFHLTSIFDHSIFEAFSRVIQKLIPQL
PTLENLLNIFCSNSLVEKAYLFDVLSKIYVATDSSPVDVQSYEICSDFIDVILDIGSIYG
RSSQLKPGHSPEILDETSSVIRLSNDLVLFLREMNQYLALICIVRADNFEKSGLIEYNVQ
CLQTAIQSIFSPRT

Sequence of entity 6 (F), FASTA

>8FW5_6 Schizosaccharomyces pombe LAM1, Human LAMTOR1 ortholog (chains F)
MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYID
GDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDFETLKV
DFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFK
KRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPPKSDLVPRGSPNSSFLFNNSDDID
EQTPLLNNDGIQRTPPSAEADMSLRKREEEEEWESKVYDVAKNKFIDVFSLRLRTEAPQR
DPRDNIYEEVLDQIDSLNLDPKYDVAKPTEQETEFIIRKLGVLIDDINNIKLSDKEIKGK
MVINLSKVQPNITGSPS

Sequence of entity 7 (G), FASTA

>8FW5_7 Schizosaccharomyces pombe LAM2, Human LAMTOR2 ortholog (chains G)
MGSSHHHHHHSLEVLFQGPGSMIKPKKLSSLMKQAVEETVPSIMVFTTTGSLLAYVSFED
PKDGLKRLDLAKRVRSIAALAGNMYSLYTATNPSPLVAESTDDVIAHQRDVLFETIIEFE
RGKLLIAAISIDGAEDKLYSKDPLLLGIVGTENAKEGMMQIKSELLKECITNELSTLGKP
V

Sequence of entity 8 (H), FASTA

>8FW5_8 Schizosaccharomyces pombe LAM3, Human LAMTOR3 ortholog (chains H)
MSVSQQLSELASKEKTVLYVADQNLEEVLCFPESTDRTTLVQLTDACLHANELAKHLEFG
KPLSITNQYSRGSCVLQIAKEKKDGSGMVVSTTIAAHNALRGALKCSNALDQVISQL

Sequence of entity 9 (I), FASTA

>8FW5_9 Schizosaccharomyces pombe LAM4, Human LAMTOR5 ortholog (chains I)
MDSQLSENLLKCVNETYRGAMLVRNGLPIATAGDVNAEEQRVICEWNSNAVSEVLHLHDS
NTKILIATKESCVLGLIYRNT

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
AF3	Aluminum fluoride	Al F3	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

Primary citation

Structure of the Schizosaccharomyces pombe Gtr-Lam complex reveals evolutionary divergence of mTORC1-dependent amino acid sensing. Tettoni, S.D., Egri, S.B., Doxsey, D.D. et al. Structure (2023) 31:1065-1076.e5. DOI 10.1016/j.str.2023.06.012 · 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
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
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

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