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- PDB-4kk0: Crystal Structure of TSC1 core domain from S. pombe -

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Basic information

Entry
Database: PDB / ID: 4kk0
TitleCrystal Structure of TSC1 core domain from S. pombe
ComponentsTuberous sclerosis 1 protein homolog
KeywordsIMMUNE SYSTEM / HEAT repeat / tumor suppressor
Function / homology
Function and homology information


positive regulation of L-methionine import across plasma membrane / Inhibition of TSC complex formation by PKB / positive regulation of L-arginine import across plasma membrane / Energy dependent regulation of mTOR by LKB1-AMPK / TP53 Regulates Metabolic Genes / TSC1-TSC2 complex / positive regulation of L-leucine import across plasma membrane / negative regulation of TOR signaling / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of TORC1 signaling ...positive regulation of L-methionine import across plasma membrane / Inhibition of TSC complex formation by PKB / positive regulation of L-arginine import across plasma membrane / Energy dependent regulation of mTOR by LKB1-AMPK / TP53 Regulates Metabolic Genes / TSC1-TSC2 complex / positive regulation of L-leucine import across plasma membrane / negative regulation of TOR signaling / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of TORC1 signaling / GTPase activator activity / regulation of cell cycle / cytoplasm
Similarity search - Function
Hamartin / Hamartin protein / Armadillo-type fold
Similarity search - Domain/homology
Tuberous sclerosis 1 protein homolog
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsSun, W. / Zhu, Y. / Wang, Z.Z. / Zhong, Q. / Gao, F. / Lou, J.Z. / Gong, W.M. / Xu, W.Q.
CitationJournal: Nat Commun / Year: 2013
Title: Crystal structure of the yeast TSC1 core domain and implications for tuberous sclerosis pathological mutations.
Authors: Sun, W. / Zhu, Y.J. / Wang, Z. / Zhong, Q. / Gao, F. / Lou, J. / Gong, W. / Xu, W.
History
DepositionMay 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tuberous sclerosis 1 protein homolog
B: Tuberous sclerosis 1 protein homolog
C: Tuberous sclerosis 1 protein homolog
D: Tuberous sclerosis 1 protein homolog
E: Tuberous sclerosis 1 protein homolog
F: Tuberous sclerosis 1 protein homolog
G: Tuberous sclerosis 1 protein homolog
H: Tuberous sclerosis 1 protein homolog
I: Tuberous sclerosis 1 protein homolog
J: Tuberous sclerosis 1 protein homolog


Theoretical massNumber of molelcules
Total (without water)537,40610
Polymers537,40610
Non-polymers00
Water00
1
A: Tuberous sclerosis 1 protein homolog
B: Tuberous sclerosis 1 protein homolog


Theoretical massNumber of molelcules
Total (without water)107,4812
Polymers107,4812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-29 kcal/mol
Surface area38130 Å2
MethodPISA
2
C: Tuberous sclerosis 1 protein homolog
D: Tuberous sclerosis 1 protein homolog


Theoretical massNumber of molelcules
Total (without water)107,4812
Polymers107,4812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-29 kcal/mol
Surface area37320 Å2
MethodPISA
3
E: Tuberous sclerosis 1 protein homolog
F: Tuberous sclerosis 1 protein homolog


Theoretical massNumber of molelcules
Total (without water)107,4812
Polymers107,4812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-29 kcal/mol
Surface area37370 Å2
MethodPISA
4
G: Tuberous sclerosis 1 protein homolog
H: Tuberous sclerosis 1 protein homolog


Theoretical massNumber of molelcules
Total (without water)107,4812
Polymers107,4812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-29 kcal/mol
Surface area37140 Å2
MethodPISA
5
I: Tuberous sclerosis 1 protein homolog
J: Tuberous sclerosis 1 protein homolog


Theoretical massNumber of molelcules
Total (without water)107,4812
Polymers107,4812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-28 kcal/mol
Surface area37430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.375, 239.791, 112.014
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Tuberous sclerosis 1 protein homolog


Mass: 53740.582 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: SPAC22F3.13, tsc1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09778

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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: 2.89 Å3/Da / Density % sol: 57.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 75mM 3Na Citrate, 25mM HEPES, 500mM NaCl, 1.5% PEI, 6.25% 2-propanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9792 Å
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 140033 / Num. obs: 140033 / % possible obs: 100 %

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.9→29.74 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 15.053 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R: 1.727 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25646 6923 5 %RANDOM
Rwork0.19202 ---
all0.19526 14858 --
obs0.19526 131073 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.428 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å20 Å2
2---4 Å2-0 Å2
3---3.7 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31897 0 0 0 31897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01932707
X-RAY DIFFRACTIONr_bond_other_d0.0010.0231299
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.96344467
X-RAY DIFFRACTIONr_angle_other_deg0.9371753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94253882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06123.3111525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.17155356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.17815220
X-RAY DIFFRACTIONr_chiral_restr0.0910.25053
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02136340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027908
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 502 -
Rwork0.289 9600 -
obs--99.84 %

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