6NZD

Cryo-EM Structure of the Lysosomal Folliculin Complex (FLCN-FNIP2-RagA-RagC-Ragulator)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural mechanism of a Rag GTPase activation checkpoint by the lysosomal folliculin complex.

Lawrence, R.E.Fromm, S.A.Fu, Y.Yokom, A.L.Kim, D.J.Thelen, A.M.Young, L.N.Lim, C.Y.Samelson, A.J.Hurley, J.H.Zoncu, R.

(2019) Science 366: 971-977

  • DOI: https://doi.org/10.1126/science.aax0364
  • Primary Citation of Related Structures:  
    6NZD

  • PubMed Abstract: 

    The tumor suppressor folliculin (FLCN) enables nutrient-dependent activation of the mechanistic target of rapamycin complex 1 (mTORC1) protein kinase via its guanosine triphosphatase (GTPase) activating protein (GAP) activity toward the GTPase RagC. Concomitant with mTORC1 inactivation by starvation, FLCN relocalizes from the cytosol to lysosomes. To determine the lysosomal function of FLCN, we reconstituted the human lysosomal FLCN complex (LFC) containing FLCN, its partner FLCN-interacting protein 2 (FNIP2), and the RagA GDP :RagC GTP GTPases as they exist in the starved state with their lysosomal anchor Ragulator complex and determined its cryo-electron microscopy structure to 3.6 angstroms. The RagC-GAP activity of FLCN was inhibited within the LFC, owing to displacement of a catalytically required arginine in FLCN from the RagC nucleotide. Disassembly of the LFC and release of the RagC-GAP activity of FLCN enabled mTORC1-dependent regulation of the master regulator of lysosomal biogenesis, transcription factor E3, implicating the LFC as a checkpoint in mTORC1 signaling.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR1166Homo sapiensMutation(s): 0 
Gene Names: LAMTOR1C11orf59PDROPP7157
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6IAA8 (Homo sapiens)
Explore Q6IAA8 
Go to UniProtKB:  Q6IAA8
PHAROS:  Q6IAA8
GTEx:  ENSG00000149357 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IAA8
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR2127Homo sapiensMutation(s): 0 
Gene Names: LAMTOR2MAPBPIPROBLD3HSPC003
Membrane Entity: Yes 
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Find proteins for Q9Y2Q5 (Homo sapiens)
Explore Q9Y2Q5 
Go to UniProtKB:  Q9Y2Q5
PHAROS:  Q9Y2Q5
GTEx:  ENSG00000116586 
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UniProt GroupQ9Y2Q5
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR3124Homo sapiensMutation(s): 0 
Gene Names: LAMTOR3MAP2K1IP1MAPKSP1PRO2783
Membrane Entity: Yes 
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Find proteins for Q9UHA4 (Homo sapiens)
Explore Q9UHA4 
Go to UniProtKB:  Q9UHA4
PHAROS:  Q9UHA4
GTEx:  ENSG00000109270 
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UniProt GroupQ9UHA4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR499Homo sapiensMutation(s): 0 
Gene Names: LAMTOR4C7orf59
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Find proteins for Q0VGL1 (Homo sapiens)
Explore Q0VGL1 
Go to UniProtKB:  Q0VGL1
PHAROS:  Q0VGL1
GTEx:  ENSG00000188186 
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UniProt GroupQ0VGL1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatitis B virus x interacting protein173Homo sapiensMutation(s): 0 
Gene Names: LAMTOR5HBXIPhCG_40252
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Find proteins for O43504 (Homo sapiens)
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PHAROS:  O43504
GTEx:  ENSG00000134248 
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UniProt GroupO43504
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related GTP-binding protein A313Homo sapiensMutation(s): 0 
Gene Names: RRAGA
Membrane Entity: Yes 
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Find proteins for Q7L523 (Homo sapiens)
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PHAROS:  Q7L523
GTEx:  ENSG00000155876 
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UniProt GroupQ7L523
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related GTP-binding protein C404Homo sapiensMutation(s): 1 
Gene Names: RRAGC
Membrane Entity: Yes 
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Find proteins for Q9HB90 (Homo sapiens)
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PHAROS:  Q9HB90
GTEx:  ENSG00000116954 
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UniProt GroupQ9HB90
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Folliculin622Homo sapiensMutation(s): 0 
Gene Names: FLCNBHD
Membrane Entity: Yes 
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Find proteins for Q8NFG4 (Homo sapiens)
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PHAROS:  Q8NFG4
GTEx:  ENSG00000154803 
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UniProt GroupQ8NFG4
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Folliculin-interacting protein 21,117Homo sapiensMutation(s): 0 
Gene Names: FNIP2FNIPLKIAA1450MAPO1
Membrane Entity: Yes 
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Find proteins for Q9P278 (Homo sapiens)
Explore Q9P278 
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PHAROS:  Q9P278
GTEx:  ENSG00000052795 
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UniProt GroupQ9P278
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L8S
Query on L8S

Download Ideal Coordinates CCD File 
K [auth G]9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione
C10 H15 N4 O14 P3 S
IAOZVDCRMYYKMQ-BZKDHIKHSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
J [auth F]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2
MODEL REFINEMENTPHENIX1.14

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States2R01GM111730-05

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence, Other