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- PDB-3voq: Crystal structure of the pleckstrin homology domain of human Sin1... -

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Basic information

Entry
Database: PDB / ID: 3voq
TitleCrystal structure of the pleckstrin homology domain of human Sin1, a TORC2 subunit
ComponentsTarget of rapamycin complex 2 subunit MAPKAP1
KeywordsMEMBRANE PROTEIN / PH domain
Function / homology
Function and homology information


TORC2 signaling / TORC2 complex / regulation of cellular response to oxidative stress / phosphatidic acid binding / phosphatidylinositol-3,4-bisphosphate binding / negative regulation of Ras protein signal transduction / phosphatidylinositol-3,5-bisphosphate binding / Constitutive Signaling by AKT1 E17K in Cancer / CD28 dependent PI3K/Akt signaling / cellular response to nutrient levels ...TORC2 signaling / TORC2 complex / regulation of cellular response to oxidative stress / phosphatidic acid binding / phosphatidylinositol-3,4-bisphosphate binding / negative regulation of Ras protein signal transduction / phosphatidylinositol-3,5-bisphosphate binding / Constitutive Signaling by AKT1 E17K in Cancer / CD28 dependent PI3K/Akt signaling / cellular response to nutrient levels / phosphatidylinositol-3,4,5-trisphosphate binding / cytoskeleton organization / substantia nigra development / phosphatidylinositol-4,5-bisphosphate binding / VEGFR2 mediated vascular permeability / small GTPase binding / Regulation of TP53 Degradation / positive regulation of peptidyl-serine phosphorylation / PIP3 activates AKT signaling / cytoplasmic vesicle / positive regulation of cell growth / molecular adaptor activity / negative regulation of apoptotic process / protein kinase binding / Golgi apparatus / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Sin1, N-terminal / Stress-activated map kinase interacting protein 1 (SIN1) / TORC2 component Sin1/Avo1 / SAPK-interacting protein 1, Pleckstrin-homology domain / Sin1, middle CRIM domain / SAPK-interacting protein 1 (Sin1), middle CRIM domain / SAPK-interacting protein 1 (Sin1), Pleckstrin-homology / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily ...Sin1, N-terminal / Stress-activated map kinase interacting protein 1 (SIN1) / TORC2 component Sin1/Avo1 / SAPK-interacting protein 1, Pleckstrin-homology domain / Sin1, middle CRIM domain / SAPK-interacting protein 1 (Sin1), middle CRIM domain / SAPK-interacting protein 1 (Sin1), Pleckstrin-homology / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Target of rapamycin complex 2 subunit MAPKAP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPan, D. / Matsuura, Y.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structures of the pleckstrin homology domain of Saccharomyces cerevisiae Avo1 and its human orthologue Sin1, an essential subunit of TOR complex 2
Authors: Pan, D. / Matsuura, Y.
History
DepositionJan 31, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Target of rapamycin complex 2 subunit MAPKAP1
B: Target of rapamycin complex 2 subunit MAPKAP1


Theoretical massNumber of molelcules
Total (without water)28,2282
Polymers28,2282
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-7 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.293, 79.293, 123.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Target of rapamycin complex 2 subunit MAPKAP1 / TORC2 subunit MAPKAP1 / Mitogen-activated protein kinase 2-associated protein 1 / Stress-activated ...TORC2 subunit MAPKAP1 / Mitogen-activated protein kinase 2-associated protein 1 / Stress-activated map kinase-interacting protein 1 / SAPK-interacting protein 1 / mSIN1


Mass: 14114.072 Da / Num. of mol.: 2 / Fragment: C-terminal PH domain, UNP residues 372-493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIN1 / Plasmid: pET30a-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)RIL / References: UniProt: Q9BPZ7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 3.44 Å3/Da / Density % sol: 64.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris, 1.26M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 2, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→41.53 Å / Num. all: 27409 / Num. obs: 27409 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.105
Reflection shellResolution: 2→2.11 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.911 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3907 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
BSSdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ULB

3ulb


Resolution: 2→41.53 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.981 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 1370 5 %RANDOM
Rwork0.1934 ---
all0.195 27409 --
obs0.195 27346 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.29 Å2 / Biso mean: 34.6473 Å2 / Biso min: 14.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---0.42 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 2→41.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1805 0 0 125 1930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.021840
X-RAY DIFFRACTIONr_angle_refined_deg2.4611.9522488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7935225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.35424.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.63615324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.928156
X-RAY DIFFRACTIONr_chiral_restr0.1990.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211347
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 82 -
Rwork0.282 1707 -
all-1789 -
obs--99.94 %

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