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(-) Description

Title :  CRYSTAL STRUCTURE OF RENAL TUMOR SUPPRESSOR PROTEIN, FOLLICULIN
 
Authors :  R. K. Nookala, D. Y. Chirgadze, T. L. Blundell
Date :  14 Dec 11  (Deposition) - 15 Aug 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Folliculin, Tumor Suppressor, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. K. Nookala, L. Langemeyer, A. Pacitto, B. Ochoa-Montano, J. C. Donaldson, B. K. Blaszczyk, D. Y. Chirgadze, F. A. Barr, J. F. Bazan, T. L. Blundell
Crystal Structure Of Folliculin Reveals A Hiddenn Function In Genetically Inherited Renal Cancer.
Open Biol V. 2 20071 2012
PubMed-ID: 22977732  |  Reference-DOI: 10.1098/RSOB.120071

(-) Compounds

Molecule 1 - FOLLICULIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETG10A
    Expression System StrainBL21 STAR
    Expression System Taxid562
    Expression System Vector TypeGATEWAY DESTINATION VECTOR
    FragmentC-TERMINAL DOMAIN, UNP RESIDUES 341-566
    GeneBHD, FLCN
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBHD SKIN LESION FIBROFOLLICULOMA PROTEIN, BIRT-HOGG-DUBE SYNDROME PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3V42)

(-) Sites  (0, 0)

(no "Site" information available for 3V42)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V42)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:479 -Pro A:480
2Gly B:479 -Pro B:480

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 10)

Asymmetric Unit (6, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_066027R362CFLCN_HUMANPolymorphism557336321A/BR362C
2UniProtVAR_025359R392GFLCN_HUMANUnclassified  ---A/BR392G
3UniProtVAR_066028H429YFLCN_HUMANDisease (PSP)375082054A/BH429Y
4UniProtVAR_025360A444SFLCN_HUMANUnclassified  ---AA444S
5UniProtVAR_025361A445TFLCN_HUMANUnclassified41419545AA445T
6UniProtVAR_066029K508RFLCN_HUMANDisease (BHD)199643834A/BK508R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_066027R362CFLCN_HUMANPolymorphism557336321AR362C
2UniProtVAR_025359R392GFLCN_HUMANUnclassified  ---AR392G
3UniProtVAR_066028H429YFLCN_HUMANDisease (PSP)375082054AH429Y
4UniProtVAR_025360A444SFLCN_HUMANUnclassified  ---AA444S
5UniProtVAR_025361A445TFLCN_HUMANUnclassified41419545AA445T
6UniProtVAR_066029K508RFLCN_HUMANDisease (BHD)199643834AK508R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_066027R362CFLCN_HUMANPolymorphism557336321BR362C
2UniProtVAR_025359R392GFLCN_HUMANUnclassified  ---BR392G
3UniProtVAR_066028H429YFLCN_HUMANDisease (PSP)375082054BH429Y
6UniProtVAR_066029K508RFLCN_HUMANDisease (BHD)199643834BK508R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (6, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_066027R362CFLCN_HUMANPolymorphism557336321A/BR362C
2UniProtVAR_025359R392GFLCN_HUMANUnclassified  ---A/BR392G
3UniProtVAR_066028H429YFLCN_HUMANDisease (PSP)375082054A/BH429Y
4UniProtVAR_025360A444SFLCN_HUMANUnclassified  ---AA444S
5UniProtVAR_025361A445TFLCN_HUMANUnclassified41419545AA445T
6UniProtVAR_066029K508RFLCN_HUMANDisease (BHD)199643834A/BK508R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V42)

(-) Exons   (0, 0)

(no "Exon" information available for 3V42)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:196
 aligned with FLCN_HUMAN | Q8NFG4 from UniProtKB/Swiss-Prot  Length:579

    Alignment length:216
                                   352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552      
           FLCN_HUMAN   343 LPVFKSLRHMRQVLGAPSFRMLAWHVLMGNQVIWKSRDVDLVQSAFEVLRTMLPVGCVRIIPYSSQYEEAYRCNFLGLSPHVQIPPHVLSSEFAVIVEVHAAARSTLHPVGCEDDQSLSKYEFVVTSGSPVAADRVGPTILNKIEAALTNQNLSVDVVDQCLVCLKEEWMNKVKVLFKFTKVDSRPKEDTQKLLSILGASEEDNVKLLKFWMTGLS 558
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhh.eeeee..........eeee......hhhhhh...eeeeeeee..-------------....eeeeeee...----...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..---.hhhhhhhhhhh...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------C-----------------------------G------------------------------------Y--------------ST--------------------------------------------------------------R-------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v42 A 343 LPVFKSLRHMRQVLGAPSFRMLAWHVLMGNQVIWKSRDVDLVQSAFEVLRTMLPVGCVRIIPYSSQYEEAYRCNFLGLSPHVQIPPHVLSSEFAVIVEVHAAA-------------SLSKYEFVVTSGSP----RVGPTILNKIEAALTNQNLSVDVVDQALVALKEEWMNKVKVLFKFTKV---PKEDTQKLLSILGASEEDNVKLLKFWMTGLS 558
                                   352       362       372       382       392       402       412       422       432       442  |      -      |462       472    |  482       492       502       512       522 |   | 532       542       552      
                                                                                                                                445           459          472  477                                            524 528                              

Chain B from PDB  Type:PROTEIN  Length:199
 aligned with FLCN_HUMAN | Q8NFG4 from UniProtKB/Swiss-Prot  Length:579

    Alignment length:216
                                   352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552      
           FLCN_HUMAN   343 LPVFKSLRHMRQVLGAPSFRMLAWHVLMGNQVIWKSRDVDLVQSAFEVLRTMLPVGCVRIIPYSSQYEEAYRCNFLGLSPHVQIPPHVLSSEFAVIVEVHAAARSTLHPVGCEDDQSLSKYEFVVTSGSPVAADRVGPTILNKIEAALTNQNLSVDVVDQCLVCLKEEWMNKVKVLFKFTKVDSRPKEDTQKLLSILGASEEDNVKLLKFWMTGLS 558
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhh.eeeee..........eeee......hhhhhh...eeeeeee.--------------......eeeeee..........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.---.hhhhhhhhhhhh...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------C-----------------------------G------------------------------------Y------------------------------------------------------------------------------R-------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v42 B 343 LPVFKSLRHMRQVLGAPSFRMLAWHVLMGNQVIWKSRDVDLVQSAFEVLRTMLPVGCVRIIPYSSQYEEAYRCNFLGLSPHVQIPPHVLSSEFAVIVEVHA--------------QSLSKYEFVVTSGSPVAADRVGPTILNKIEAALTNQNLSVDVVDQALVALKEEWMNKVKVLFKFTK---RPKEDTQKLLSILGASEEDNVKLLKFWMTGLS 558
                                   352       362       372       382       392       402       412       422       432       442|        -     | 462       472       482       492       502       512       522|   |  532       542       552      
                                                                                                                              443            458                                                              523 527                               

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3V42)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V42)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V42)

(-) Gene Ontology  (39, 39)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FLCN_HUMAN | Q8NFG4)
molecular function
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0031929    TOR signaling    A series of molecular signals mediated by TOR (Target of rapamycin) proteins, members of the phosphoinositide (PI) 3-kinase related kinase (PIKK) family that act as serine/threonine kinases in response to nutrient availability or growth factors.
    GO:0007043    cell-cell junction assembly    The aggregation, arrangement and bonding together of a set of components to form a junction between cells.
    GO:0030097    hemopoiesis    The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:2001170    negative regulation of ATP biosynthetic process    Any process that stops, prevents or reduces the frequency, rate or extent of ATP biosynthetic process.
    GO:0070373    negative regulation of ERK1 and ERK2 cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0035024    negative regulation of Rho protein signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of Rho protein signal transduction.
    GO:0032007    negative regulation of TOR signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of TOR signaling.
    GO:0030308    negative regulation of cell growth    Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
    GO:0030336    negative regulation of cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
    GO:1901723    negative regulation of cell proliferation involved in kidney development    Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation involved in kidney development.
    GO:2000506    negative regulation of energy homeostasis    Any process that stops, prevents or reduces the frequency, rate or extent of energy homeostasis.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0010823    negative regulation of mitochondrion organization    Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion.
    GO:0051898    negative regulation of protein kinase B signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:1900181    negative regulation of protein localization to nucleus    Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleus.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0032008    positive regulation of TOR signaling    Any process that activates or increases the frequency, rate or extent of TOR signaling.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0010508    positive regulation of autophagy    Any process that activates, maintains or increases the rate of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:0045785    positive regulation of cell adhesion    Any process that activates or increases the frequency, rate or extent of cell adhesion.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0030511    positive regulation of transforming growth factor beta receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of TGF-beta receptor signaling pathway activity.
    GO:0032006    regulation of TOR signaling    Any process that modulates the frequency, rate or extent of TOR signaling.
    GO:0032465    regulation of cytokinesis    Any process that modulates the frequency, rate or extent of the division of the cytoplasm of a cell and its separation into two daughter cells.
    GO:0035065    regulation of histone acetylation    Any process that modulates the frequency, rate or extent of the addition of an acetyl group to a histone protein.
    GO:2000973    regulation of pro-B cell differentiation    Any process that modulates the frequency, rate or extent of pro-B cell differentiation.
    GO:0001932    regulation of protein phosphorylation    Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein.
cellular component
    GO:0044291    cell-cell contact zone    Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions, e.g., the intercalated disk of muscle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0030496    midbody    A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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