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- PDB-2xs6: CRYSTAL STRUCTURE OF THE RHOGAP DOMAIN OF HUMAN PIK3R2 -

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Basic information

Entry
Database: PDB / ID: 2xs6
TitleCRYSTAL STRUCTURE OF THE RHOGAP DOMAIN OF HUMAN PIK3R2
ComponentsPHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT BETA
KeywordsTRANSFERASE / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


IRS-mediated signalling / regulation of actin filament polymerization / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / regulation of stress fiber assembly / Co-stimulation by ICOS / RHOD GTPase cycle / RHOF GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / Nephrin family interactions ...IRS-mediated signalling / regulation of actin filament polymerization / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / regulation of stress fiber assembly / Co-stimulation by ICOS / RHOD GTPase cycle / RHOF GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / Nephrin family interactions / Signaling by LTK in cancer / Signaling by LTK / PI3K/AKT activation / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / Signaling by ALK / RHOB GTPase cycle / RHOJ GTPase cycle / intracellular glucose homeostasis / Synthesis of PIPs at the plasma membrane / RHOU GTPase cycle / CDC42 GTPase cycle / RET signaling / T cell differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / CD28 dependent PI3K/Akt signaling / RHOA GTPase cycle / RAC2 GTPase cycle / Role of LAT2/NTAL/LAB on calcium mobilization / RAC3 GTPase cycle / Interleukin receptor SHC signaling / Role of phospholipids in phagocytosis / negative regulation of MAPK cascade / regulation of protein localization to plasma membrane / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / GPVI-mediated activation cascade / Tie2 Signaling / RAC1 GTPase cycle / phosphotyrosine residue binding / Interleukin-7 signaling / positive regulation of cell adhesion / Downstream signal transduction / B cell differentiation / response to endoplasmic reticulum stress / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Regulation of signaling by CBL / Signaling by SCF-KIT / receptor tyrosine kinase binding / VEGFA-VEGFR2 Pathway / positive regulation of protein import into nucleus / cellular response to insulin stimulus / Constitutive Signaling by Aberrant PI3K in Cancer / Signaling by ALK fusions and activated point mutants / insulin receptor signaling pathway / DAP12 signaling / protein transport / Downstream TCR signaling / PIP3 activates AKT signaling / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / protein phosphatase binding / G alpha (q) signalling events / Extra-nuclear estrogen signaling / regulation of autophagy / immune response / protein heterodimerization activity / focal adhesion / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Phosphatidylinositol 3-kinase regulatory subunit beta, SH3 domain / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. ...Phosphatidylinositol 3-kinase regulatory subunit beta, SH3 domain / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphatidylinositol 3-kinase regulatory subunit beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsTresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / van der Berg, S. / Wahlberg, E. / Weigelt, J. / Nordlund, P.
CitationJournal: FEBS J. / Year: 2016
Title: The Structure and Catalytic Mechanism of Human Sphingomyelin Phosphodiesterase Like 3A - an Acid Sphingomyelinase Homolog with a Novel Nucleotide Hydrolase Activity.
Authors: Lim, S.M. / Yeung, K. / Tresaugues, L. / Ling, T.H. / Nordlund, P.
History
DepositionSep 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Apr 6, 2016Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9882
Polymers22,9531
Non-polymers351
Water1,45981
1
A: PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT BETA
hetero molecules

A: PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9774
Polymers45,9062
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1630 Å2
ΔGint-33 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.661, 34.354, 71.317
Angle α, β, γ (deg.)90.00, 130.88, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2025-

HOH

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Components

#1: Protein PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT BETA / PHOSPHATIDYLINOSITOL 3-KINASE 85 KDA REGULATORY SUBUNIT BETA / PTDINS-3-KINASE REGULATORY SUBUNIT ...PHOSPHATIDYLINOSITOL 3-KINASE 85 KDA REGULATORY SUBUNIT BETA / PTDINS-3-KINASE REGULATORY SUBUNIT BETA / PI3-KINASE REGULATORY SUBUNIT BETA / PI3K REGULATORY SUBUNIT BETA / PTDINS-3-KINASE REGULATORY SUBUNIT P85-BETA / PI3-KINASE SUBUNIT P85-BETA


Mass: 22953.043 Da / Num. of mol.: 1 / Fragment: RHOGAP DOMAIN, RESIDUES 108-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)R3 PRARE / References: UniProt: O00459
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 1.91 Å3/Da / Density % sol: 35.7 % / Description: NONE
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 0.1 M NACL, 0.85 M TRI-SODIUM CITRATE DIHYDRATE AND 0.1 M SODIUM CACODYLATE PH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 17, 2010 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.09→47.33 Å / Num. obs: 9968 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.9
Reflection shellResolution: 2.09→2.21 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.7 / % possible all: 76.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PBW

1pbw


Resolution: 2.09→53.92 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.903 / SU B: 10.993 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 563 5.6 %RANDOM
Rwork0.19149 ---
obs0.1942 9404 95.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.775 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å21.22 Å2
2--1.09 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.09→53.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1276 0 1 81 1358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221311
X-RAY DIFFRACTIONr_bond_other_d0.0010.02916
X-RAY DIFFRACTIONr_angle_refined_deg1.0322.0241799
X-RAY DIFFRACTIONr_angle_other_deg0.84732241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0165165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.01522.54951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4815199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7221513
X-RAY DIFFRACTIONr_chiral_restr0.0490.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02242
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_it0.3251.5846
X-RAY DIFFRACTIONr_mcbond_other0.0671.5316
X-RAY DIFFRACTIONr_mcangle_it0.60821368
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9853465
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6464.5430
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.094→2.148 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 26 -
Rwork0.24 461 -
obs--65.11 %
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)
15.8262-0.0326-1.07294.7497-0.66843.9099-0.0644-0.0044-0.2163-0.118-0.0475-0.32170.02870.46740.11190.0955-0.02370.01220.0697-0.00320.1004-12.0329.794124.0523
27.4469-1.20524.52053.1979-3.159610.4285-0.24110.32560.146-0.1106-0.1203-0.1059-0.03440.16620.36150.07310.00420.03010.0204-0.02260.1058-13.58097.754319.0275
35.8123.858-15.11010.0084-3.873525.95380.56640.9798-0.1193-0.4264-0.07710.1316-1.7793-1.1173-0.48930.46850.1444-0.15060.45770.14570.8135-13.623617.6935-0.0837
416.1777-1.5597-0.29342.07550.68623.0201-0.11730.60170.913-0.09710.0253-0.073-0.27520.30.0920.1256-0.04090.00460.05490.06060.1059-6.737516.499415.0912
58.2242.59951.21338.4412-1.88358.35-0.23520.86710.1421-0.52770.17120.00970.08090.50250.0640.1459-0.00420.02860.21730.00040.0606-6.366710.69926.635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A109 - 160
2X-RAY DIFFRACTION2A161 - 194
3X-RAY DIFFRACTION3A195 - 212
4X-RAY DIFFRACTION4A213 - 242
5X-RAY DIFFRACTION5A243 - 294

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