6CES: GATOR1-RAG
Cryo-EM structure of GATOR1-RAG. Determined by electron microscopy at 4.0 Å resolution. Released 28 Mar 2018.
- Method
- Electron microscopy
- Resolution
- 4.0 Å
- Organism
- Homo sapiens
- Chains
- 5
- Atoms
- 18,988
- Mol. weight
- 370.31 kDa
- Ligands
- GNP
- Released
- 28 Mar 2018
Explore 6CES in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6CES contains 81 α-helices and 97 β-strands across 5 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: 10 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-14 | 7 | 18 |
| α-helix | 22-27 | 6 | |
| α-helix | 35-38 | 4 | |
| β-strand | 45-52 | 8 | 18 |
| β-strand | 56-63 | 8 | 18 |
| α-helix | 67-74 | 8 | |
| α-helix | 78-81 | 4 | |
| β-strand | 87-92 | 6 | 18 |
| α-helix | 99-114 | 16 | |
| β-strand | 121-126 | 6 | 18 |
| α-helix | 134-151 | 18 | |
| β-strand | 157-161 | 5 | 18 |
| α-helix | 168-180 | 13 | |
| α-helix | 185-197 | 13 | |
| β-strand | 202-207 | 6 | 25 |
| β-strand | 213-218 | 6 | 25 |
| α-helix | 226-243 | 18 | |
| β-strand | 251-256 | 6 | 25 |
| β-strand | 259-265 | 7 | 25 |
| β-strand | 270-275 | 6 | 25 |
| α-helix | 284-297 | 14 | |
Chain C: 11 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 75-85 | 11 | |
| α-helix | 90-93 | 4 | |
| α-helix | 103-110 | 8 | |
| α-helix | 127-133 | 7 | |
| β-strand | 141-144 | 4 | 26 |
| α-helix | 151-155 | 5 | |
| α-helix | 157-167 | 11 | |
| β-strand | 171-177 | 7 | 26 |
| α-helix | 187-197 | 11 | |
| β-strand | 209-215 | 7 | 26 |
| α-helix | 226-234 | 9 | |
| α-helix | 241-250 | 10 | |
| β-strand | 259-262 | 4 | 25 |
| α-helix | 281-297 | 17 | |
| β-strand | 315-320 | 6 | 25 |
| β-strand | 324-330 | 7 | 25 |
| β-strand | 336-339 | 4 | 25 |
| β-strand | 341 | 1 | 25 |
| α-helix | 353-366 | 14 | |
Chain D: 25 helices, 52 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 39-42 | 4 | 11 |
| β-strand | 53-56 | 4 | 11 |
| α-helix | 71-75 | 5 | |
| β-strand | 89-90 | 2 | 11 |
| β-strand | 96 | 1 | 12 |
| β-strand | 99-104 | 6 | 13 |
| α-helix | 111-120 | 10 | |
| β-strand | 123-127 | 5 | 12 |
| β-strand | 131-134 | 4 | 13 |
| β-strand | 137-146 | 10 | 13 |
| β-strand | 149-150 | 2 | 13 |
| β-strand | 153-157 | 5 | 12 |
| β-strand | 161-166 | 6 | 13 |
| β-strand | 170-176 | 7 | 14 |
| β-strand | 184 | 1 | 15 |
| β-strand | 190 | 1 | 15 |
| α-helix | 191-193 | 3 | |
| α-helix | 194-200 | 7 | |
| α-helix | 201-209 | 9 | |
| β-strand | 215-225 | 11 | 14 |
| α-helix | 234-236 | 3 | |
| β-strand | 238-242 | 5 | 14 |
| β-strand | 247-262 | 16 | 14 |
| α-helix | 269-286 | 18 | |
| 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 | 405-407 | 3 | 14 |
| β-strand | 424 | 1 | 4 |
| α-helix | 745-748 | 4 | |
| α-helix | 750 | 1 | |
| β-strand | 751 | 1 | 13 |
| α-helix | 752-753 | 2 | |
| β-strand | 756 | 1 | 17 |
| β-strand | 770-774 | 5 | 17 |
| β-strand | 775 | 1 | 18 |
| α-helix | 798-805 | 8 | |
| α-helix | 813-814 | 2 | |
| β-strand | 818 | 1 | 19 |
| β-strand | 825 | 1 | 20 |
| β-strand | 834 | 1 | 20 |
| β-strand | 835-836 | 2 | 14 |
| β-strand | 841 | 1 | 19 |
| β-strand | 852-858 | 7 | 17 |
| β-strand | 862-868 | 7 | 17 |
| β-strand | 872-877 | 6 | 17 |
| α-helix | 976-990 | 15 | |
| β-strand | 993-994 | 2 | 17 |
| α-helix | 1090-1101 | 12 | |
| α-helix | 1180-1184 | 5 | |
| β-strand | 1194 | 1 | 21 |
| β-strand | 1204 | 1 | 21 |
| α-helix | 1207-1217 | 11 | |
| α-helix | 1223-1231 | 9 | |
| β-strand | 1243 | 1 | 22 |
| β-strand | 1245 | 1 | 22 |
| β-strand | 1293-1300 | 8 | 23 |
| α-helix | 1304-1311 | 8 | |
| β-strand | 1352-1357 | 6 | 23 |
| β-strand | 1369-1374 | 6 | 23 |
| β-strand | 1384-1390 | 7 | 23 |
| α-helix | 1395-1410 | 16 | |
| β-strand | 1415-1418 | 4 | 23 |
| α-helix | 1425-1426 | 2 | |
| β-strand | 1439-1441 | 3 | 24 |
| α-helix | 1465-1483 | 19 | |
| β-strand | 1487-1489 | 3 | 24 |
| β-strand | 1501-1504 | 4 | 24 |
| β-strand | 1509-1512 | 4 | 24 |
| β-strand | 1546-1550 | 5 | 24 |
| α-helix | 1567-1580 | 14 | |
| α-helix | 1586-1595 | 10 | |
Chain M: 20 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 9-11 | 3 | 1 |
| β-strand | 30 | 1 | 5 |
| β-strand | 33 | 1 | 5 |
| β-strand | 47-49 | 3 | 6 |
| β-strand | 53-55 | 3 | 6 |
| α-helix | 64-73 | 10 | |
| β-strand | 83-86 | 4 | 1 |
| β-strand | 92-96 | 5 | 1 |
| β-strand | 99 | 1 | 7 |
| β-strand | 123 | 1 | 7 |
| β-strand | 126-130 | 5 | 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 | 258-269 | 12 | |
| α-helix | 293-304 | 12 | |
| β-strand | 308-310 | 3 | 8 |
| β-strand | 311-316 | 6 | 9 |
| α-helix | 337-345 | 9 | |
| α-helix | 355-358 | 4 | |
| α-helix | 364-378 | 15 | |
| α-helix | 382-386 | 5 | |
| α-helix | 391-393 | 3 | |
| α-helix | 395-401 | 7 | |
| β-strand | 405-410 | 6 | 9 |
| β-strand | 430-432 | 3 | 8 |
| β-strand | 451 | 1 | 10 |
| β-strand | 456 | 1 | 10 |
| α-helix | 477-485 | 9 | |
| α-helix | 493-500 | 8 | |
| α-helix | 515-519 | 5 | |
| α-helix | 524-531 | 8 | |
| α-helix | 539-545 | 7 | |
| α-helix | 559-566 | 8 | |
Chain N: 15 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-15 | 9 | 1 |
| β-strand | 22-27 | 6 | 1 |
| α-helix | 40-45 | 6 | |
| β-strand | 59-61 | 3 | 1 |
| β-strand | 66-75 | 10 | 1 |
| β-strand | 81-90 | 10 | 1 |
| α-helix | 99-115 | 17 | |
| α-helix | 118-120 | 3 | |
| α-helix | 122-141 | 20 | |
| β-strand | 144-148 | 5 | 2 |
| β-strand | 154-158 | 5 | 2 |
| β-strand | 174-177 | 4 | 3 |
| α-helix | 181-183 | 3 | |
| β-strand | 184 | 1 | 4 |
| α-helix | 191-196 | 6 | |
| α-helix | 197-200 | 4 | |
| α-helix | 205-208 | 4 | |
| α-helix | 209-213 | 5 | |
| α-helix | 217-230 | 14 | |
| β-strand | 232-235 | 4 | 3 |
| α-helix | 255-263 | 9 | |
| α-helix | 275-285 | 11 | |
| α-helix | 324-326 | 3 | |
| α-helix | 352-358 | 7 | |
| α-helix | 362-368 | 7 | |
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) |
| Ras-related GTP-binding protein A | A | protein | 313 | Homo sapiens | Q7L523 (AlphaFold model) |
| Ras-related GTP-binding protein C | C | protein | 399 | Homo sapiens | Q9HB90 |
Sequence of entity 1 (N), FASTA
>6CES_1 GATOR complex protein NPRL2 (chains N)
MGSGCRIECIFFSEFHPTLGPKITYQVPEDFISRELFDTVQVYIITKPELQNKLITVTAM
EKKLIGCPVCIEHKKYSRNALLFNLGFVCDAQAKTCALEPIVKKLAGYLTTLELESSFVS
MEESKQKLVPIMTILLEELNASGRCTLPIDESNTIHLKVIEQRPDPPVAQEYDVPVFTKD
KEDFFNSQWDLTTQQILPYIDGFRHIQKISAEADVELNLVRIAIQNLLYYGVVTLVSILQ
YSNVYCPTPKVQDLVDDKSLQEACLSYVTKQGHKRASLRDVFQLYCSLSPGTTVRDLIGR
HPQQLQHVDERKLIQFGLMKNLIRRLQKYPVRVTREEQSHPARLYTGCHSYDEICCKTGM
SYHELDERLENDPNIIICWK
Sequence of entity 2 (M), FASTA
>6CES_2 GATOR complex protein NPRL3 (chains M)
MRDNTSPISVILVSSGSRGNKLLFRYPFQRSQEHPASQTSKPRSRYAASNTGDHADEQDG
DSRFSDVILATILATKSEMCGQKFELKIDNVRFVGHPTLLQHALGQISKTDPSPKREAPT
MILFNVVFALRANADPSVINCLHNLSRRIATVLQHEERRCQYLTREAKLILALQDEVSAM
ADGNEGPQSPFHHILPKCKLARDLKEAYDSLCTSGVVRLHINSWLEVSFCLPHKIHYAAS
SLIPPEAIERSLKAIRPYHALLLLSDEKSLLGELPIDCSPALVRVIKTTSAVKNLQQLAQ
DADLALLQVFQLAAHLVYWGKAIIIYPLCENNVYMLSPNASVCLYSPLAEQFSHQFPSHD
LPSVLAKFSLPVSLSEFRNPLAPAVQETQLIQMVVWMLQRRLLIQLHTYVCLMASPSEEE
PRPREDDVPFTARVGGRSLSTPNALSFGSPTSSDDMTLTSPSMDNSSAELLPSGDSPLNQ
RMTENLLASLSEHERAAILSVPAAQNPEDLRMFARLLHYFRGRHHLEEIMYNENTRRSQL
LMLFDKFRSVLVVTTHEDPVIAVFQALLP
Sequence of entity 3 (D), FASTA
>6CES_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
Sequence of entity 4 (A), FASTA
>6CES_4 Ras-related GTP-binding protein A (chains A)
MPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNL
WDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDA
KIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECACFRTSIWDETLYKAWSSIVYQL
IPNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHYQCKEQRDVHRFEKISNIIKQFKL
SCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKL
ERVDGPKHSLLMR
Sequence of entity 5 (C), FASTA
>6CES_5 Ras-related GTP-binding protein C (chains C)
MSLQYGAEETPLAGSYGAADSFPKDFGYGVEEEEEEAAAAGGGVGAGAGGGCGPGGADSS
KPRILLMGLRRSGKNSIQKVVFHKMSPNETLFLESTNKIYKDDISNSSFVNFQIWDFPGQ
MDFFDPTFDYEMIFRGTGALIYVIDAQDDYMEALTRLHITVSKAYKVNPDMNFEVFIHKV
DGLSDDHKIETQRDIHQRANDDLADAGLEKLHLSFYLTSIYDHSIFEAFSKVVQKLIPQL
PTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDVSCIYG
LKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYNFHCFR
KAIHEVFEVGVTSHRSCGHQTSASSLKALTHNGTPRNAI
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GNP | Phosphoaminophosphonic acid-guanylate ester | C10 H17 N6 O13 P3 | 1 |
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
- 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
Browse structure collections
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