6NZD: Lysosomal Folliculin Complex
Cryo-EM Structure of the Lysosomal Folliculin Complex (FLCN-FNIP2-RagA-RagC-Ragulator). Determined by electron microscopy at 3.6 Å resolution. Released 6 Nov 2019.
- Method
- Electron microscopy
- Resolution
- 3.6 Å
- Organism
- Homo sapiens
- Chains
- 9
- Atoms
- 13,633
- Mol. weight
- 348.52 kDa
- Ligands
- L8S, GDP
- Released
- 6 Nov 2019
Explore 6NZD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6NZD contains 76 α-helices and 65 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: 7 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 49-64 | 16 | |
| α-helix | 66-67 | 2 | |
| α-helix | 98-102 | 5 | |
| α-helix | 115-120 | 6 | |
| α-helix | 122-125 | 4 | |
| α-helix | 126-142 | 17 | |
| α-helix | 143-145 | 3 | |
| β-strand | 155 | 1 | 1 |
Chain B: 3 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 1 |
| α-helix | 4-12 | 9 | |
| β-strand | 19-25 | 7 | 2 |
| β-strand | 31-36 | 6 | 2 |
| α-helix | 42-60 | 19 | |
| β-strand | 71-76 | 6 | 2 |
| β-strand | 79-86 | 8 | 2 |
| β-strand | 89-95 | 7 | 2 |
| α-helix | 101-122 | 22 | |
Chain C: 6 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-12 | 9 | |
| α-helix | 13-15 | 3 | |
| β-strand | 19-25 | 7 | 2 |
| β-strand | 31-36 | 6 | 2 |
| α-helix | 42-45 | 4 | |
| α-helix | 47-50 | 4 | |
| α-helix | 52-60 | 9 | |
| β-strand | 68-74 | 7 | 2 |
| β-strand | 78-85 | 8 | 2 |
| β-strand | 88-95 | 8 | 2 |
| α-helix | 100-119 | 20 | |
Chain D: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-10 | 7 | |
| β-strand | 15-22 | 8 | 3 |
| β-strand | 25-31 | 7 | 3 |
| α-helix | 37-52 | 16 | |
| β-strand | 65-69 | 5 | 3 |
| β-strand | 73-80 | 8 | 3 |
| β-strand | 83-90 | 8 | 3 |
Chain E: 5 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 85-95 | 11 | |
| β-strand | 100-106 | 7 | 3 |
| β-strand | 112-117 | 6 | 3 |
| α-helix | 121-123 | 3 | |
| α-helix | 124-134 | 11 | |
| α-helix | 135-137 | 3 | |
| α-helix | 144-145 | 2 | |
| β-strand | 146-151 | 6 | 3 |
| β-strand | 154-161 | 8 | 3 |
| β-strand | 164-170 | 7 | 3 |
Chain F: 7 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11-14 | 4 | 4 |
| α-helix | 22-27 | 6 | |
| β-strand | 59-60 | 2 | 4 |
| β-strand | 88-93 | 6 | 4 |
| α-helix | 99-115 | 17 | |
| β-strand | 124-127 | 4 | 4 |
| α-helix | 134-151 | 18 | |
| β-strand | 159-161 | 3 | 4 |
| α-helix | 168-180 | 13 | |
| α-helix | 184-198 | 15 | |
| β-strand | 202-207 | 6 | 5 |
| β-strand | 213-217 | 5 | 5 |
| α-helix | 228-243 | 16 | |
| β-strand | 249-255 | 7 | 5 |
| β-strand | 260-267 | 8 | 5 |
| β-strand | 270-276 | 7 | 5 |
| α-helix | 283-294 | 12 | |
Chain G: 12 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 63-66 | 4 | 6 |
| α-helix | 74-83 | 10 | |
| α-helix | 89-91 | 3 | |
| α-helix | 94-96 | 3 | |
| β-strand | 100-103 | 4 | 6 |
| β-strand | 113-116 | 4 | 6 |
| α-helix | 130-135 | 6 | |
| β-strand | 141-145 | 5 | 6 |
| α-helix | 151-165 | 15 | |
| β-strand | 174-178 | 5 | 6 |
| α-helix | 185-204 | 20 | |
| β-strand | 214-217 | 4 | 6 |
| α-helix | 224-236 | 13 | |
| α-helix | 240-253 | 14 | |
| β-strand | 258-263 | 6 | 5 |
| β-strand | 269-272 | 4 | 5 |
| α-helix | 276-278 | 3 | |
| α-helix | 279-299 | 21 | |
| β-strand | 315-320 | 6 | 5 |
| β-strand | 324-330 | 7 | 5 |
| β-strand | 335-342 | 8 | 5 |
| α-helix | 343-346 | 4 | |
| α-helix | 349-366 | 18 | |
Chain H: 17 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-9 | 6 | 7 |
| β-strand | 11 | 1 | 8 |
| β-strand | 15 | 1 | 8 |
| β-strand | 18-20 | 3 | 7 |
| β-strand | 23 | 1 | 7 |
| α-helix | 115-131 | 17 | |
| β-strand | 139-145 | 7 | 7 |
| β-strand | 149-156 | 8 | 7 |
| β-strand | 170-176 | 7 | 7 |
| α-helix | 179-184 | 6 | |
| α-helix | 186-208 | 23 | |
| α-helix | 242-245 | 4 | |
| α-helix | 250-266 | 17 | |
| α-helix | 349-356 | 8 | |
| α-helix | 358-369 | 12 | |
| β-strand | 373-377 | 5 | 9 |
| α-helix | 381-391 | 11 | |
| α-helix | 392-394 | 3 | |
| α-helix | 397-399 | 3 | |
| β-strand | 402-406 | 5 | 9 |
| β-strand | 417-420 | 4 | 9 |
| α-helix | 428-431 | 4 | |
| β-strand | 436-442 | 7 | 9 |
| β-strand | 464-469 | 6 | 9 |
| α-helix | 472 | 1 | |
| α-helix | 481-491 | 11 | |
| α-helix | 497-521 | 25 | |
| α-helix | 529-538 | 10 | |
| α-helix | 544-553 | 10 | |
| α-helix | 554-556 | 3 | |
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 |
|---|
| Ragulator complex protein LAMTOR1 | A | protein | 166 | Homo sapiens | Q6IAA8 (AlphaFold model) |
| Ragulator complex protein LAMTOR2 | B | protein | 127 | Homo sapiens | Q9Y2Q5 (AlphaFold model) |
| Ragulator complex protein LAMTOR3 | C | protein | 124 | Homo sapiens | Q9UHA4 (AlphaFold model) |
| Ragulator complex protein LAMTOR4 | D | protein | 99 | Homo sapiens | Q0VGL1 (AlphaFold model) |
| Hepatitis B virus x interacting protein | E | protein | 173 | Homo sapiens | O43504 |
| Ras-related GTP-binding protein A | F | protein | 313 | Homo sapiens | Q7L523 |
| Ras-related GTP-binding protein C | G | protein | 404 | Homo sapiens | Q9HB90 |
| Folliculin | H | protein | 622 | Homo sapiens | Q8NFG4 |
| Folliculin-interacting protein 2 | I | protein | 1117 | Homo sapiens | Q9P278 |
Sequence of entity 1 (A), FASTA
>6NZD_1 Ragulator complex protein LAMTOR1 (chains A)
SNAEFMACCYSSENEDSDQDREERKLLLDPSSPPTKALNGAEPNYHSLPSARTDEQALLS
SILAKTASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQP
HQVLASEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGIP
Sequence of entity 2 (B), FASTA
>6NZD_2 Ragulator complex protein LAMTOR2 (chains B)
GAMLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDR
NGNQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEP
LTQVAAS
Sequence of entity 3 (C), FASTA
>6NZD_3 Ragulator complex protein LAMTOR3 (chains C)
MADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQG
SKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQV
VEVS
Sequence of entity 4 (D), FASTA
>6NZD_4 Ragulator complex protein LAMTOR4 (chains D)
MTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMN
VPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV
Sequence of entity 5 (E), FASTA
>6NZD_5 Hepatitis B virus x interacting protein (chains E)
MEPGAGHLDGHRAGSPSLRQALCDGSAVMFSSKERGRCTVINFVPLEAPLRSTPRSRQVT
EACGGEGRAVPLGSEPEWSVGGMEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLS
DEHAGVISVLAQQAAKLTSDPTDIPVVCLESDNGNIMIQKHDGITVAVHKMAS
Sequence of entity 6 (F), FASTA
>6NZD_6 Ras-related GTP-binding protein A (chains F)
MPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNL
WDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDA
KIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECACFRTSIWDETLYKAWSSIVYQL
IPNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHYQCKEQRDVHRFEKISNIIKQFKL
SCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKL
ERVDGPKHSLLMR
Sequence of entity 7 (G), FASTA
>6NZD_7 Ras-related GTP-binding protein C (chains G)
GADSRMSLQYGAEETPLAGSYGAADSFPKDFGYGVEEEEEEAAAAGGGVGAGAGGGCGPG
GADSSKPRILLMGLRRSGKSSIQKVVFHKMSPNETLFLESTNKIYKDDISNSSFVNFQIW
DFPGQMDFFDPTFDYEMIFRGTGALIYVIDAQDDYMEALTRLHITVSKAYKVNPDMNFEV
FIHKVNGLSDDHKIETQRDIHQRANDDLADAGLEKLHLSFYLTSIYDHSIFEAFSKVVQK
LIPQLPTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDV
SCIYGLKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYN
FHCFRKAIHEVFEVGVTSHRSCGHQTSASSLKALTHNGTPRNAI
Sequence of entity 8 (H), FASTA
>6NZD_8 Folliculin (chains H)
MASWSHPQFEKGGGARGGSGGGSWSHPQFEKGFDYKDDDDKGTMNAIVALCHFCELHGPR
TLFCTEVLHAPLPQGDGNEDSPGQGEQAEEEEGGIQMNSRMRAHSPAEGASVESSSPGPK
KSDMCEGCRSLAAGHPGYISHDKETSIKYVSHQHPSHPQLFSIVRQACVRSLSCEVCPGR
EGPIFFGDEQHGFVFSHTFFIKDSLARGFQRWYSIITIMMDRIYLINSWPFLLGKVRGII
DELQGKALKVFEAEQFGCPQRAQRMNTAFTPFLHQRNGNAARSLTSLTSDDNLWACLHTS
FAWLLKACGSRLTEKLLEGAPTEDTLVQMEKLADLEEESESWDNSEAEEEEKAPVLPEST
EGRELTQGPAESSSLSGCGSWQPRKLPVFKSLRHMRQVLGAPSFRMLAWHVLMGNQVIWK
SRDVDLVQSAFEVLRTMLPVGCVRIIPYSSQYEEAYRCNFLGLSPHVQIPPHVLSSEFAV
IVEVHAAARSTLHPVGCEDDQSLSKYEFVVTSGSPVAADRVGPTILNKIEAALTNQNLSV
DVVDQCLVCLKEEWMNKVKVLFKFTKVDSRPKEDTQKLLSILGASEEDNVKLLKFWMTGL
SKTYKSHLMSTVRSPTASESRN
Sequence of entity 9 (I), FASTA
>6NZD_9 Folliculin-interacting protein 2 (chains I)
GGTMAPTLLQKLFNKRGSSGSSAAASAQGRAPKEGPAFSWSCSEFDLNEIRLIVYQDCDR
RGRQVLFDSKAVQKIEEVTAQKTEDVPIKISAKCCQGSSSVSSSSSSSISSHSSSGGSSH
HAKEQLPKYQYTRPASDVNMLGEMMFGSVAMSYKGSTLKIHYIRSPPQLMISKVFSARMG
SFCGSTNNLQDSFEYINQDPNLGKLNTNQNSLGPCRTGSNLAHSTPVDMPSRGQNEDRDS
GIARSASLSSLLITPFPSPSSSTSSSSSYQRRWLRSQTTSLENGIIPRRSTDETFSLAEE
TCSSNPAMVRRKKIAISIIFSLCEKEEAQRNFQDFFFSHFPLFESHMNRLKSAIEKAMIS
CRKIAESSLRVQFYVSRLMEALGEFRGTIWNLYSVPRIAEPVWLTMMSGTLEKNQLCQRF
LKEFTLLIEQINKNQFFAALLTAVLTYHLAWVPTVMPVDHPPIKAFSEKRTSQSVNMLAK
THPYNPLWAQLGDLYGAIGSPVRLTRTVVVGKQKDLVQRILYVLTYFLRCSELQENQLTW
SGNHGEGDQVLNGSKIITALEKGEVEESEYVVITVRNEPALVPPILPPTAAERHNPWPTG
FPECPEGTDSRDLGLKPDKEANRRPEQGSEACSAGCLGPASDASWKPQNAFCGDEKNKEA
PQDGSSRLPSCEVLGAGMKMDQQAVCELLKVEMPTRLPDRSVAWPCPDRHLREKPSLEKV
TFQIGSFASPESDFESRMKKMEERVKACGPSLEASEAADVAQDPQVSRSPFKPGFQENVC
CPQNRLSEGDEGESDKGFAEDRGSRNDMAADIAGQLSHAADLGTASHGAGGTGGRRLEAT
RGLYVKAAEGPVLEPVAPRCVQRGPGLVAGANIPCGDDNKKANFRTEGDIPRNESSDSAL
GDSDDEACASAMLDLGHGGDRTGGSLEVELPLPRSQSISTQNVRNFGRSLLAGYCPTYMP
DLVLHGTGSDEKLKQCLVADLVHTVHHPVLDEPIAEAVCIIADTDKWSVQVATSQRKVTD
NMKLGQDVLVSSQVSSLLQSILQLYKLHLPADFCIMHLEDRLQEMYLKSKMLSEYLRGHT
RVHVKELGVVLGIESNDLPLLTAIASTHSPYVAQILL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| L8S | 9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-al… | C10 H15 N4 O14 P3 S | 1 |
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 1 |
Primary citation
Structural mechanism of a Rag GTPase activation checkpoint by the lysosomal folliculin complex. Lawrence, R.E., Fromm, S.A., Fu, Y. et al. Science (2019) 366:971-977. DOI 10.1126/science.aax0364 · PubMed
Other PDB entries of the same protein (UniProt Q6IAA8 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6B9X 1.42 Å, Crystal structure of Ragulator
- 5X6V 2.02 Å, Crystal structure of human heteroheptameric complex
- 6EHP 2.3 Å, The crystal structure of the human LAMTOR complex
- 5X6U 2.4 Å, Crystal structure of human heteropentameric complex
- 5Y39 2.65 Å, Crystal structure of Ragulator complex (p18 76-145)
- 6EHR 2.9 Å, The crystal structure of the human LAMTOR-RagA CTD-RagC CTD complex
- 5Y3A 2.9 Å, Crystal structure of Ragulator complex (p18 49-161)
- 7UX2 2.9 Å, cryo-EM structure of the Raptor-TFEB-Rag-Ragulator complex
- 5YK3 3.01 Å, human 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
Browse structure collections
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