6CET: GATOR1

Cryo-EM structure of GATOR1. Determined by electron microscopy at 4.4 Å resolution. Released 28 Mar 2018.

Method: Electron microscopy
Resolution: 4.4 Å
Organism: Homo sapiens
Chains: 3
Atoms: 14,012
Mol. weight: 288.87 kDa
Released: 28 Mar 2018

Explore 6CET in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6CET contains 59 α-helices and 75 β-strands across 3 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 D: 24 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	39-42	4	11
β-strand	53-56	4	11
α-helix	72-75	4
α-helix	88	1
β-strand	89-90	2	11
β-strand	99-104	6	12
α-helix	111-119	9
β-strand	123-127	5	13
β-strand	131-134	4	12
β-strand	137-146	10	12
β-strand	149-150	2	12
β-strand	153-157	5	13
β-strand	161-166	6	12
β-strand	168-176	9	14
β-strand	184	1	15
β-strand	190	1	15
α-helix	191-193	3
α-helix	194-200	7
α-helix	201-210	10
β-strand	213-225	13	14
α-helix	234-236	3
β-strand	238-241	4	14
β-strand	248-262	15	14
α-helix	269-279	11
α-helix	281-286	6
β-strand	295-296	2	14
α-helix	306-317	12
β-strand	331-337	7	14
β-strand	342-345	4	16
α-helix	347-357	11
β-strand	363-367	5	14
β-strand	379-382	4	16
β-strand	397-398	2	16
β-strand	404-407	4	14
β-strand	424	1	5
α-helix	745-748	4
β-strand	751	1	12
β-strand	756-757	2	17
β-strand	770-774	5	17
α-helix	798-805	8
β-strand	818	1	18
β-strand	825	1	19
β-strand	834	1	19
β-strand	835-836	2	14
β-strand	841	1	18
β-strand	853-858	6	17
β-strand	862-868	7	17
β-strand	871-876	6	17
α-helix	976-988	13
β-strand	993-995	3	17
α-helix	1088-1101	14
α-helix	1180-1184	5
α-helix	1186-1188	3
β-strand	1194	1	20
β-strand	1204	1	20
α-helix	1207-1216	10
α-helix	1223-1231	9
β-strand	1293-1300	8	21
α-helix	1304-1311	8
β-strand	1352-1357	6	21
β-strand	1369-1374	6	21
β-strand	1384-1390	7	21
α-helix	1395-1410	16
β-strand	1415-1418	4	21
β-strand	1439-1441	3	22
α-helix	1465-1483	19
β-strand	1487-1489	3	22
β-strand	1501-1504	4	22
β-strand	1509-1512	4	22
β-strand	1546-1550	5	22
α-helix	1567-1578	12
α-helix	1586-1595	10

Chain M: 22 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	1
β-strand	30	1	6
β-strand	33	1	6
β-strand	44	1	1
β-strand	47-48	2	7
β-strand	54-55	2	7
α-helix	65-74	10
β-strand	84-86	3	1
β-strand	92-94	3	1
β-strand	127-130	4	1
α-helix	136-149	14
α-helix	161-172	12
α-helix	189-194	6
α-helix	204-212	9
α-helix	246-251	6
α-helix	257-268	12
α-helix	275-278	4
α-helix	293-306	14
β-strand	309-310	2	8
β-strand	312-316	5	9
α-helix	337-345	9
α-helix	348-358	11
α-helix	364-378	15
α-helix	382-386	5
α-helix	392-401	10
α-helix	404	1
β-strand	405-409	5	9
β-strand	430-431	2	8
β-strand	451	1	10
β-strand	456	1	10
α-helix	477-485	9
α-helix	492-498	7
α-helix	514-519	6
α-helix	524-531	8
α-helix	538-545	8
α-helix	547-549	3
α-helix	560-566	7

Chain N: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	1
β-strand	22-27	6	1
α-helix	40-46	7
α-helix	47-50	4
β-strand	59-61	3	1
β-strand	63	1	2
β-strand	66	1	2
β-strand	67-75	9	1
β-strand	81-89	9	1
α-helix	99-116	18
α-helix	122-141	20
β-strand	144-148	5	3
β-strand	154-158	5	3
β-strand	174-177	4	4
α-helix	181-183	3
β-strand	184	1	5
α-helix	191-196	6
α-helix	205-208	4
α-helix	209-213	5
α-helix	217-230	14
β-strand	232-235	4	4
α-helix	255-263	9
α-helix	275-285	11
α-helix	352-358	7
α-helix	362-366	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GATOR complex protein NPRL2	N	protein	380	Homo sapiens	Q8WTW4 (AlphaFold model)
GATOR complex protein NPRL3	M	protein	569	Homo sapiens	Q12980 (AlphaFold model)
GATOR complex protein DEPDC5	D	protein	1603	Homo sapiens	O75140 (AlphaFold model)

Sequence of entity 1 (N), FASTA

>6CET_1 GATOR complex protein NPRL2 (chains N)
MGSGCRIECIFFSEFHPTLGPKITYQVPEDFISRELFDTVQVYIITKPELQNKLITVTAM
EKKLIGCPVCIEHKKYSRNALLFNLGFVCDAQAKTCALEPIVKKLAGYLTTLELESSFVS
MEESKQKLVPIMTILLEELNASGRCTLPIDESNTIHLKVIEQRPDPPVAQEYDVPVFTKD
KEDFFNSQWDLTTQQILPYIDGFRHIQKISAEADVELNLVRIAIQNLLYYGVVTLVSILQ
YSNVYCPTPKVQDLVDDKSLQEACLSYVTKQGHKRASLRDVFQLYCSLSPGTTVRDLIGR
HPQQLQHVDERKLIQFGLMKNLIRRLQKYPVRVTREEQSHPARLYTGCHSYDEICCKTGM
SYHELDERLENDPNIIICWK

Sequence of entity 2 (M), FASTA

>6CET_2 GATOR complex protein NPRL3 (chains M)
MRDNTSPISVILVSSGSRGNKLLFRYPFQRSQEHPASQTSKPRSRYAASNTGDHADEQDG
DSRFSDVILATILATKSEMCGQKFELKIDNVRFVGHPTLLQHALGQISKTDPSPKREAPT
MILFNVVFALRANADPSVINCLHNLSRRIATVLQHEERRCQYLTREAKLILALQDEVSAM
ADGNEGPQSPFHHILPKCKLARDLKEAYDSLCTSGVVRLHINSWLEVSFCLPHKIHYAAS
SLIPPEAIERSLKAIRPYHALLLLSDEKSLLGELPIDCSPALVRVIKTTSAVKNLQQLAQ
DADLALLQVFQLAAHLVYWGKAIIIYPLCENNVYMLSPNASVCLYSPLAEQFSHQFPSHD
LPSVLAKFSLPVSLSEFRNPLAPAVQETQLIQMVVWMLQRRLLIQLHTYVCLMASPSEEE
PRPREDDVPFTARVGGRSLSTPNALSFGSPTSSDDMTLTSPSMDNSSAELLPSGDSPLNQ
RMTENLLASLSEHERAAILSVPAAQNPEDLRMFARLLHYFRGRHHLEEIMYNENTRRSQL
LMLFDKFRSVLVVTTHEDPVIAVFQALLP

Sequence of entity 3 (D), FASTA

>6CET_3 GATOR complex protein DEPDC5 (chains D)
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

Primary citation

Architecture of the human GATOR1 and GATOR1-Rag GTPases complexes. Shen, K., Huang, R.K., Brignole, E.J. et al. Nature (2018) 556:64-69. DOI 10.1038/nature26158 · 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
7T3C 4.0 Å, GATOR1-RAG-RAGULATOR - Dual Complex
9O5E 5.0 Å, The dimeric KICSTOR-GATOR1 supercomplex

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