3V42 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

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

Molecule 1 - FOLLICULIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETG10A
	Expression System Strain	:	BL21 STAR
	Expression System Taxid	:	562
	Expression System Vector Type	:	GATEWAY DESTINATION VECTOR
	Fragment	:	C-TERMINAL DOMAIN, UNP RESIDUES 341-566
	Gene	:	BHD, FLCN
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BHD SKIN LESION FIBROFOLLICULOMA PROTEIN, BIRT-HOGG-DUBE SYNDROME PROTEIN

		1	2
Asymmetric Unit	:	A	B
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)

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

(no "Site" information available for 3V42)

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

Asymmetric Unit

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

Asymmetric Unit (6, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_066027	R	362	C	FLCN_HUMAN	Polymorphism	557336321	A/B	R	362	C
2	UniProt	VAR_025359	R	392	G	FLCN_HUMAN	Unclassified	---	A/B	R	392	G
3	UniProt	VAR_066028	H	429	Y	FLCN_HUMAN	Disease (PSP)	375082054	A/B	H	429	Y
4	UniProt	VAR_025360	A	444	S	FLCN_HUMAN	Unclassified	---	A	A	444	S
5	UniProt	VAR_025361	A	445	T	FLCN_HUMAN	Unclassified	41419545	A	A	445	T
6	UniProt	VAR_066029	K	508	R	FLCN_HUMAN	Disease (BHD)	199643834	A/B	K	508	R

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

Biological Unit 1 (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_066027	R	362	C	FLCN_HUMAN	Polymorphism	557336321	A	R	362	C
2	UniProt	VAR_025359	R	392	G	FLCN_HUMAN	Unclassified	---	A	R	392	G
3	UniProt	VAR_066028	H	429	Y	FLCN_HUMAN	Disease (PSP)	375082054	A	H	429	Y
4	UniProt	VAR_025360	A	444	S	FLCN_HUMAN	Unclassified	---	A	A	444	S
5	UniProt	VAR_025361	A	445	T	FLCN_HUMAN	Unclassified	41419545	A	A	445	T
6	UniProt	VAR_066029	K	508	R	FLCN_HUMAN	Disease (BHD)	199643834	A	K	508	R

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

Biological Unit 2 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_066027	R	362	C	FLCN_HUMAN	Polymorphism	557336321	B	R	362	C
2	UniProt	VAR_025359	R	392	G	FLCN_HUMAN	Unclassified	---	B	R	392	G
3	UniProt	VAR_066028	H	429	Y	FLCN_HUMAN	Disease (PSP)	375082054	B	H	429	Y
6	UniProt	VAR_066029	K	508	R	FLCN_HUMAN	Disease (BHD)	199643834	B	K	508	R

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

Biological Unit 3 (6, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_066027	R	362	C	FLCN_HUMAN	Polymorphism	557336321	A/B	R	362	C
2	UniProt	VAR_025359	R	392	G	FLCN_HUMAN	Unclassified	---	A/B	R	392	G
3	UniProt	VAR_066028	H	429	Y	FLCN_HUMAN	Disease (PSP)	375082054	A/B	H	429	Y
4	UniProt	VAR_025360	A	444	S	FLCN_HUMAN	Unclassified	---	A	A	444	S
5	UniProt	VAR_025361	A	445	T	FLCN_HUMAN	Unclassified	41419545	A	A	445	T
6	UniProt	VAR_066029	K	508	R	FLCN_HUMAN	Disease (BHD)	199643834	A/B	K	508	R

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

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

(no "Exon" information available for 3V42)

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 '\|'

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

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

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

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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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3v42)

	Sites
(no "Sites" information available for 3v42)

	Cis Peptide Bonds
		Gly A:479 - Pro A:480	[ RasMol ]
		Gly B:479 - Pro B:480	[ RasMol ]

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	3v42
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Ligands, Modified Residues, Ions (0, 0)

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