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- PDB-5okm: Crystal structure of human SHIP2 Phosphatase-C2 -

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Basic information

Entry
Database: PDB / ID: 5okm
TitleCrystal structure of human SHIP2 Phosphatase-C2
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
KeywordsHYDROLASE / SHIP2 / Phosphatase / C2 / phosphatidylinositol (3 / 4 / 5)-triphosphate
Function / homology
Function and homology information


negative regulation of insulin-like growth factor receptor signaling pathway / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / inositol-polyphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / ruffle assembly / regulation of actin filament organization / phosphatidylinositol dephosphorylation / endochondral ossification / phosphatidylinositol biosynthetic process / immune system process ...negative regulation of insulin-like growth factor receptor signaling pathway / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / inositol-polyphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / ruffle assembly / regulation of actin filament organization / phosphatidylinositol dephosphorylation / endochondral ossification / phosphatidylinositol biosynthetic process / immune system process / Synthesis of IP3 and IP4 in the cytosol / establishment of mitotic spindle orientation / Synthesis of PIPs at the plasma membrane / regulation of immune response / Interleukin receptor SHC signaling / ERK1 and ERK2 cascade / SH2 domain binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / basal plasma membrane / post-embryonic development / filopodium / actin filament organization / response to insulin / spindle pole / SH3 domain binding / endocytosis / glucose metabolic process / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of protein localization / lamellipodium / actin binding / gene expression / cell adhesion / nuclear speck / negative regulation of cell population proliferation / negative regulation of gene expression / apoptotic process / Golgi apparatus / nucleus / cytosol
Similarity search - Function
Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / SAM domain (Sterile alpha motif) / Endonuclease/exonuclease/phosphatase superfamily / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / SAM domain (Sterile alpha motif) / Endonuclease/exonuclease/phosphatase superfamily / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsLe Coq, J. / Lietha, D.
CitationJournal: Elife / Year: 2017
Title: Structural basis for interdomain communication in SHIP2 providing high phosphatase activity.
Authors: Le Coq, J. / Camacho-Artacho, M. / Velazquez, J.V. / Santiveri, C.M. / Gallego, L.H. / Campos-Olivas, R. / Dolker, N. / Lietha, D.
History
DepositionJul 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
B: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
C: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
D: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
E: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
F: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
G: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
H: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)425,40838
Polymers422,0048
Non-polymers3,40430
Water28,1751564
1
A: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4058
Polymers52,7511
Non-polymers6557
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2816
Polymers52,7511
Non-polymers5315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1574
Polymers52,7511
Non-polymers4063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3437
Polymers52,7511
Non-polymers5936
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0332
Polymers52,7511
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2816
Polymers52,7511
Non-polymers5315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8132
Polymers52,7511
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0953
Polymers52,7511
Non-polymers3442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.037, 175.836, 176.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 / Inositol polyphosphate phosphatase-like protein 1 / INPPL-1 / Protein 51C / SH2 domain-containing ...Inositol polyphosphate phosphatase-like protein 1 / INPPL-1 / Protein 51C / SH2 domain-containing inositol 5'-phosphatase 2 / SHIP-2


Mass: 52750.504 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: The two first residues are from the expression vector
Source: (gene. exp.) Homo sapiens (human) / Gene: INPPL1, SHIP2 / Plasmid: pOPINJ / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS
References: UniProt: O15357, phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase
#2: Chemical
ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1564 / 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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.1 M BisTris propane pH 7, 0.2 M NaNO3, 20% PEG 3350, 0.025% CH2Cl2, 2 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.96→48.97 Å / Num. obs: 287002 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rpim(I) all: 0.033 / Net I/σ(I): 14.8
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.1 / CC1/2: 0.743 / Rpim(I) all: 0.368 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NR8

3nr8


Resolution: 1.96→48.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.466 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.134 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 15180 5 %RANDOM
Rwork0.1795 ---
obs0.18091 287002 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.654 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å20 Å2
2---0.15 Å20 Å2
3---1.27 Å2
Refinement stepCycle: 1 / Resolution: 1.96→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28047 0 225 1564 29836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01929007
X-RAY DIFFRACTIONr_bond_other_d0.0020.0226443
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.94839239
X-RAY DIFFRACTIONr_angle_other_deg1.2413.00261374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19853473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21523.8351408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.663154995
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.69615191
X-RAY DIFFRACTIONr_chiral_restr0.0770.24293
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0231858
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026217
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_it1.382.1313875
X-RAY DIFFRACTIONr_mcbond_other1.382.1313874
X-RAY DIFFRACTIONr_mcangle_it2.423.17617302
X-RAY DIFFRACTIONr_mcangle_other2.423.17717303
X-RAY DIFFRACTIONr_scbond_it1.3462.34615132
X-RAY DIFFRACTIONr_scbond_other1.3462.34615132
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3623.43421920
X-RAY DIFFRACTIONr_long_range_B_refined5.62224.57831304
X-RAY DIFFRACTIONr_long_range_B_other5.61424.25431066
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 1083 -
Rwork0.276 21111 -
obs--99.99 %
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)
10.2534-0.11370.15620.5673-0.14150.78470.00470.02510.03440.01340.0585-0.03850.0965-0.0829-0.06310.34880.01560.0050.25450.01910.0945.89442.35429.838
20.52260.1757-0.08710.3129-0.08290.87690.031-0.08840.0366-0.0468-0.0496-0.0581-0.0489-0.10430.01860.33160.04280.04760.25880.01730.11318.4958.00563.222
30.3972-0.1050.09560.60.14190.78720.11660.09160.0509-0.0369-0.1078-0.0408-0.03060.0256-0.00880.35580.06770.04310.28050.01210.073866.01745.95229.647
40.82220.53750.43380.74570.14330.61190.251-0.06570.06660.1038-0.0520.06240.1447-0.0334-0.1990.3872-0.0506-0.01370.1534-0.02220.1694-26.8868.77116.146
50.5724-0.115-0.05580.7772-0.19440.4686-0.04330.02410.04790.117-0.0379-0.00530.02970.01840.08120.38630.02760.02750.17090.01320.148128.233104.0812.496
60.4398-0.08520.03180.9936-0.30060.3539-0.0421-0.0311-0.0273-0.22290.0556-0.11120.0863-0.0559-0.01360.41990.03940.0760.15260.01230.152127.18571.112-14.055
70.4931-0.20220.02910.6290.31950.8423-0.06930.0265-0.01370.1167-0.08710.1197-0.01380.0970.15640.351-0.01960.00020.159-0.02270.193535.747-12.830.887
80.51130.13560.02130.27940.01410.87370.0658-0.0601-0.0635-0.0306-0.101-0.01560.01570.06480.03520.33420.0247-0.03780.26390.00140.106762.28127.05861.36
91.9252-0.275-0.68981.57421.13240.9455-0.0141-0.0177-0.16450.0396-0.05430.03250.0409-0.01520.06840.42840.06040.05880.1502-0.01340.135822.5117.34915.858
102.2962-1.62890.6792.3185-1.03021.17020.10630.30750.2474-0.0486-0.0134-0.1056-0.06940.1177-0.09290.32750.00150.08710.27280.0710.156839.55161.6750.691
116.43433.7429-1.01846.2528-2.51411.4092-0.1093-0.23290.7057-0.31380.06660.6071-0.2048-0.05570.04270.59810.1716-0.14590.18530.06920.304752.23573.74617.689
121.4921-0.1606-1.11451.05450.71841.51710.0926-0.17360.14430.0446-0.185-0.0038-0.09340.09990.09240.3811-0.0351-0.03170.2012-0.05010.17933.24182.70919.312
133.3263-1.8361-1.33531.64182.09733.4891-0.2518-0.2632-0.17890.13060.21150.07460.04380.17190.04030.70360.23770.12440.24120.01020.037411.042116.27627.992
141.92230.4566-0.81450.7486-0.73031.1903-0.0770.29380.312-0.017-0.09450.03930.0277-0.10370.17150.3770.0371-0.09570.24630.01780.2785-4.65381.546-17.305
154.0347-1.67231.44871.5532-2.58965.12530.1321-0.4418-0.0551-0.10280.21860.17520.1443-0.1948-0.35070.59810.009-0.10960.29050.09690.07848.502-27.85127.421
161.3818-0.8983-0.27631.13170.29280.60920.12710.1854-0.218-0.097-0.01180.2335-0.0180.0445-0.11540.32490.0328-0.08310.2555-0.05260.176831.11425.11449.76
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A420 - 732
2X-RAY DIFFRACTION2B420 - 731
3X-RAY DIFFRACTION3C420 - 731
4X-RAY DIFFRACTION4D421 - 731
5X-RAY DIFFRACTION5E420 - 731
6X-RAY DIFFRACTION6F421 - 731
7X-RAY DIFFRACTION7G421 - 731
8X-RAY DIFFRACTION8H422 - 731
9X-RAY DIFFRACTION9A746 - 875
10X-RAY DIFFRACTION10B745 - 874
11X-RAY DIFFRACTION11C744 - 875
12X-RAY DIFFRACTION12D745 - 874
13X-RAY DIFFRACTION13E746 - 873
14X-RAY DIFFRACTION14F746 - 874
15X-RAY DIFFRACTION15G746 - 874
16X-RAY DIFFRACTION16H746 - 874

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