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- PDB-3ulc: Crystal structure of the pleckstrin homology domain of Saccharomy... -

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Basic information

Entry
Database: PDB / ID: 3ulc
TitleCrystal structure of the pleckstrin homology domain of Saccharomyces cerevisiae Avo1, a TORC2 subunit, in the P3121 crystal form
ComponentsTarget of rapamycin complex 2 subunit AVO1
KeywordsMEMBRANE PROTEIN / PH domain / membrane localization
Function / homology
Function and homology information


PIP3 activates AKT signaling / CD28 dependent PI3K/Akt signaling / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Regulation of TP53 Degradation / establishment or maintenance of actin cytoskeleton polarity / VEGFR2 mediated vascular permeability / TORC2 signaling / TORC2 complex / vacuolar membrane / TOR signaling ...PIP3 activates AKT signaling / CD28 dependent PI3K/Akt signaling / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Regulation of TP53 Degradation / establishment or maintenance of actin cytoskeleton polarity / VEGFR2 mediated vascular permeability / TORC2 signaling / TORC2 complex / vacuolar membrane / TOR signaling / phosphatidylinositol-4,5-bisphosphate binding / regulation of cell growth / molecular adaptor activity / plasma membrane / cytoplasm
Similarity search - Function
: / AVO1 ubiquitin-like domain / 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 ...: / AVO1 ubiquitin-like domain / 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 AVO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
DepositionNov 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Target of rapamycin complex 2 subunit AVO1


Theoretical massNumber of molelcules
Total (without water)14,6091
Polymers14,6091
Non-polymers00
Water362
1
A: Target of rapamycin complex 2 subunit AVO1

A: Target of rapamycin complex 2 subunit AVO1


Theoretical massNumber of molelcules
Total (without water)29,2172
Polymers29,2172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area4350 Å2
ΔGint-14 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.917, 60.917, 84.096
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Target of rapamycin complex 2 subunit AVO1 / TORC2 subunit AVO1 / Adheres voraciously to TOR2 protein 1


Mass: 14608.734 Da / Num. of mol.: 1 / Fragment: PH domain, residues 1056-1176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: AVO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08236
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.08 Å3/Da / Density % sol: 60.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Tris-HCl, 6% PEG8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2009
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→32.88 Å / Num. all: 4709 / Num. obs: 4563 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.051
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 3.7 / % possible all: 84

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Processing

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

3ulb


Resolution: 2.8→28.64 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.838 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2888 206 4.5 %RANDOM
Rwork0.2436 ---
all0.2455 4709 --
obs0.2455 4563 96.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.71 Å2 / Biso mean: 57.7293 Å2 / Biso min: 24.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.12 Å20 Å2
2--0.23 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.8→28.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 0 0 2 808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02823
X-RAY DIFFRACTIONr_angle_refined_deg1.9051.9321113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.496597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35322.10538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.14215137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.609157
X-RAY DIFFRACTIONr_chiral_restr0.1050.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021613
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 12 -
Rwork0.359 220 -
all-232 -
obs--78.91 %

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