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- PDB-3nr8: Crystal structure of human SHIP2 -

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Basic information

Entry
Database: PDB / ID: 3nr8
TitleCrystal structure of human SHIP2
ComponentsPhosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2
KeywordsHYDROLASE / Structural Genomics Consortium / SGC / Phosphatidylinositol-3 / 4 / 5-trisphosphate 5-phosphatase 2 / SHIP2 / INPPL1 / SHIP-2 / Phosphatidylinositol / phosphatase / signalling / magnesium / structural genomics consortium stockholm / magnesium binding
Function / homology
Function and homology information


negative regulation of insulin-like growth factor receptor signaling pathway / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / inositol-polyphosphate 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 / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / inositol-polyphosphate 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 / SH2 domain binding / basal plasma membrane / post-embryonic development / filopodium / actin filament organization / response to insulin / SH3 domain binding / spindle pole / endocytosis / glucose metabolic process / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of protein localization / lamellipodium / actin binding / cell adhesion / nuclear speck / negative regulation of cell population proliferation / negative regulation of gene expression / 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
Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2014
Title: Structural basis for phosphoinositide substrate recognition, catalysis, and membrane interactions in human inositol polyphosphate 5-phosphatases
Authors: Tresaugues, L. / Silvander, C. / Flodin, S. / Welin, M. / Nyman, T. / Graslund, S. / Hammarstrom, M. / Berglund, H. / Nordlund, P.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 28, 2014Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
B: Phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2
A: Phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5233
Polymers72,4882
Non-polymers351
Water64936
1
B: Phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2792
Polymers36,2441
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2


Theoretical massNumber of molelcules
Total (without water)36,2441
Polymers36,2441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.796, 61.177, 114.320
Angle α, β, γ (deg.)90.00, 91.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

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Components

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


Mass: 36243.852 Da / Num. of mol.: 2 / Fragment: Phosphatase domain, UNP residues 419-732
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INPPL1, SHIP2 / Plasmid: pNIC-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: O15357, alkaline phosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20% PEG 6000, 0.1M citric acid pH 5, 2mM biphenyl 2,3',4,5',6-pentakisphosphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 22, 2010 / Details: mirrors
RadiationMonochromator: Si-111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.8→44.77 Å / Num. all: 15400 / Num. obs: 15338 / % possible obs: 99.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 59.7 Å2 / Rmerge(I) obs: 0.152 / Rsym value: 0.152 / Net I/σ(I): 7.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2 / Num. unique all: 2227 / Rsym value: 0.72 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I9Y

1i9y


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.853 / SU B: 43.322 / SU ML: 0.389 / Cross valid method: THROUGHOUT / ESU R Free: 0.448 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27247 755 4.9 %RANDOM
Rwork0.21358 ---
all0.21644 14621 --
obs0.21644 14524 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.337 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å22.19 Å2
2---0.38 Å20 Å2
3---1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4784 0 1 36 4821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224914
X-RAY DIFFRACTIONr_bond_other_d0.0010.023330
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9386670
X-RAY DIFFRACTIONr_angle_other_deg0.80738066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2885586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21523.529238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57515816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7521533
X-RAY DIFFRACTIONr_chiral_restr0.0650.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215419
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021054
X-RAY DIFFRACTIONr_mcbond_it0.2451.52942
X-RAY DIFFRACTIONr_mcbond_other0.0461.51196
X-RAY DIFFRACTIONr_mcangle_it0.47124784
X-RAY DIFFRACTIONr_scbond_it0.70231972
X-RAY DIFFRACTIONr_scangle_it1.2014.51885
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1283TIGHT POSITIONAL0.150.05
589MEDIUM POSITIONAL0.240.5
1723LOOSE POSITIONAL0.285
1283TIGHT THERMAL0.20.5
589MEDIUM THERMAL0.242
1723LOOSE THERMAL0.2810
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 59 -
Rwork0.321 1010 -
obs-1010 99.44 %
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)
14.468-0.04930.60123.0876-0.4122.55260.0172-0.4163-0.4846-0.02940.02420.21110.3544-0.2581-0.04140.16-0.01290.00960.50140.18890.140926.3148-4.6436105.9959
228.043612.57-3.46716.4819-2.00910.67690.9411-1.9602-2.5140.3555-1.5858-1.817-0.10640.62290.64480.34730.0117-0.12991.38280.56170.85943.10615.1519112.0532
33.3396-0.18660.74212.8499-0.62142.49430.05090.06460.1058-0.19420.0771-0.0439-0.0476-0.1693-0.1280.1890.00920.02150.36430.14050.113225.38027.963695.2061
44.6805-1.35620.73994.543-1.64183.3629-0.18010.04470.31-0.09170.35120.234-0.34260.0015-0.17110.1908-0.02270.04620.03810.03570.280240.279539.225666.7306
525.3347-5.91435.729528.05855.64913.12631.0220.8915-0.0599-2.9693-1.0676-0.0105-0.5185-0.06420.04560.82860.2974-0.31140.880.56290.980321.52847.660872.0083
64.1095-1.29291.26674.8663-3.45466.0096-0.0705-0.4662-0.26860.10860.27150.3275-0.0618-0.2053-0.2010.17490.01870.07490.05730.03240.227240.888728.29778.3432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B420 - 575
2X-RAY DIFFRACTION2B576 - 596
3X-RAY DIFFRACTION3B597 - 731
4X-RAY DIFFRACTION4A421 - 581
5X-RAY DIFFRACTION5A582 - 591
6X-RAY DIFFRACTION6A594 - 731

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