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- PDB-3v42: Crystal structure of renal tumor suppressor protein, folliculin -

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Basic information

Entry
Database: PDB / ID: 3v42
TitleCrystal structure of renal tumor suppressor protein, folliculin
ComponentsFolliculin
KeywordsPROTEIN BINDING / folliculin / tumor suppressor
Function / homology
Function and homology information


negative regulation of cell proliferation involved in kidney development / negative regulation of mitochondrial DNA metabolic process / negative regulation of muscle tissue development / negative regulation of post-translational protein modification / cell proliferation involved in kidney development / : / negative regulation of brown fat cell differentiation / negative regulation of cellular respiration / FNIP-folliculin RagC/D GAP / regulation of Ras protein signal transduction ...negative regulation of cell proliferation involved in kidney development / negative regulation of mitochondrial DNA metabolic process / negative regulation of muscle tissue development / negative regulation of post-translational protein modification / cell proliferation involved in kidney development / : / negative regulation of brown fat cell differentiation / negative regulation of cellular respiration / FNIP-folliculin RagC/D GAP / regulation of Ras protein signal transduction / : / negative regulation of lysosome organization / negative regulation of ATP biosynthetic process / regulation of pro-B cell differentiation / regulation of TOR signaling / Amino acids regulate mTORC1 / lysosome localization / negative regulation of TOR signaling / enzyme inhibitor activity / cell-cell junction assembly / negative regulation of glycolytic process / negative regulation of cold-induced thermogenesis / negative regulation of protein localization to nucleus / negative regulation of Rho protein signal transduction / TOR signaling / positive regulation of transforming growth factor beta receptor signaling pathway / hemopoiesis / positive regulation of cell adhesion / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of TOR signaling / positive regulation of autophagy / energy homeostasis / positive regulation of intrinsic apoptotic signaling pathway / ERK1 and ERK2 cascade / positive regulation of TORC1 signaling / cellular response to amino acid starvation / cellular response to starvation / GTPase activator activity / intrinsic apoptotic signaling pathway / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cytokinesis / epithelial cell proliferation / regulation of protein phosphorylation / cilium / negative regulation of ERK1 and ERK2 cascade / mitotic spindle / negative regulation of epithelial cell proliferation / in utero embryonic development / lysosome / positive regulation of protein phosphorylation / positive regulation of apoptotic process / lysosomal membrane / negative regulation of gene expression / centrosome / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Folliculin / Rossmann fold - #12430 / Folliculin / Folliculin, DENN domain / Folliculin, DENN domain, C-terminal superfamily / Folliculin C-terminal domain / Folliculin/SMCR8, longin domain / Folliculin/SMCR8, tripartite DENN domain / Vesicle coat protein involved in Golgi to plasma membrane transport / Tripartite DENN FLCN/SMCR8-type domain profile. ...Folliculin / Rossmann fold - #12430 / Folliculin / Folliculin, DENN domain / Folliculin, DENN domain, C-terminal superfamily / Folliculin C-terminal domain / Folliculin/SMCR8, longin domain / Folliculin/SMCR8, tripartite DENN domain / Vesicle coat protein involved in Golgi to plasma membrane transport / Tripartite DENN FLCN/SMCR8-type domain profile. / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNookala, R.K. / Chirgadze, D.Y. / Blundell, T.L.
CitationJournal: Open Biol / Year: 2012
Title: Crystal structure of folliculin reveals a hidDENN function in genetically inherited renal cancer.
Authors: Nookala, R.K. / Langemeyer, L. / Pacitto, A. / Ochoa-Montano, B. / Donaldson, J.C. / Blaszczyk, B.K. / Chirgadze, D.Y. / Barr, F.A. / Bazan, J.F. / Blundell, T.L.
History
DepositionDec 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Folliculin
B: Folliculin


Theoretical massNumber of molelcules
Total (without water)50,9332
Polymers50,9332
Non-polymers00
Water4,035224
1
A: Folliculin


Theoretical massNumber of molelcules
Total (without water)25,4671
Polymers25,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Folliculin


Theoretical massNumber of molelcules
Total (without water)25,4671
Polymers25,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Folliculin

B: Folliculin


Theoretical massNumber of molelcules
Total (without water)50,9332
Polymers50,9332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645-x+3/2,y-1/2,-z+1/21
Buried area1950 Å2
ΔGint-14 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.050, 99.951, 107.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Folliculin / / BHD skin lesion fibrofolliculoma protein / Birt-Hogg-Dube syndrome protein


Mass: 25466.611 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, UNP RESIDUES 341-566 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BHD, FLCN / Plasmid: PETG10A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR / References: UniProt: Q8NFG4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 MM BIS-TRIS, PH5.5, 200 MM LISO4, 25% PEG 3350, VAPOR DIFFUSION, TEMPERATURE 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.92→29.85 Å / Num. obs: 35477 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 14.3
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.648 / % possible all: 61.2

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Processing

Software
NameVersionClassification
DNAdata collection
PHENIXmodel building
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEMET STRUCTURE OF FOLLICULIN COLLECTED AT 2.9A

Resolution: 2→29.14 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.707 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1570 5 %RANDOM
Rwork0.204 ---
obs0.207 29744 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3078 0 0 224 3302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223150
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.9594278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6155390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03323.71124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.37415538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0411517
X-RAY DIFFRACTIONr_chiral_restr0.1340.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212299
X-RAY DIFFRACTIONr_mcbond_it1.2541.51975
X-RAY DIFFRACTIONr_mcangle_it2.14523195
X-RAY DIFFRACTIONr_scbond_it3.46731175
X-RAY DIFFRACTIONr_scangle_it5.4014.51082
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 100 -
Rwork0.249 2084 -
obs--95.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.45710.22610.22720.4515-0.53091.35580.0063-0.0052-0.00650.10380.0020.0029-0.2150.0156-0.00830.0624-0.0039-0.00120.04490.00970.037959.912422.258439.2068
20.67350.28440.04722.9140.15580.01160.0322-0.0076-0.03190.1025-0.01550.11640.0074-0.0006-0.01670.02270.0023-0.00350.03470.01370.06259.43120.337640.7193
30.10260.0515-0.27740.9683-0.66831.2018-0.04260.0056-0.0027-0.09030.0877-0.04720.118-0.0193-0.0450.0339-0.0260.01280.0521-0.00630.053661.114418.547912.3337
40.27420.71090.18482.3220.07860.4612-0.0098-0.01070.05670.08610.05970.2529-0.0885-0.0895-0.04990.0428-0.00680.01660.05520.02520.060956.401140.115215.0934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A343 - 471
2X-RAY DIFFRACTION2A472 - 558
3X-RAY DIFFRACTION3B343 - 497
4X-RAY DIFFRACTION4B498 - 558

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