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- PDB-6squ: Crystal structure of human SHIP2 catalytic domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 6squ
TitleCrystal structure of human SHIP2 catalytic domain in complex with 1,2,4 Dimer
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
KeywordsHYDROLASE
Function / homology
Function and homology information


negative regulation of insulin-like growth factor receptor signaling pathway / inositol-polyphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / ruffle assembly / phosphatidylinositol dephosphorylation / regulation of actin filament organization / endochondral ossification / phosphatidylinositol biosynthetic process / Synthesis of IP3 and IP4 in the cytosol ...negative regulation of insulin-like growth factor receptor signaling pathway / inositol-polyphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / ruffle assembly / phosphatidylinositol dephosphorylation / regulation of actin filament organization / endochondral ossification / phosphatidylinositol biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / Synthesis of PIPs at the plasma membrane / establishment of mitotic spindle orientation / immune system process / Interleukin receptor SHC signaling / regulation of immune response / ERK1 and ERK2 cascade / SH2 domain binding / basal plasma membrane / actin filament organization / post-embryonic development / filopodium / phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to insulin / SH3 domain binding / glucose metabolic process / endocytosis / Signaling by CSF1 (M-CSF) in myeloid cells / spindle pole / lamellipodium / regulation of protein localization / 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
SHIP1/2 second C2 domain / SHIP1/2 first C2 domain / Inositol polyphosphate-related phosphatase / Endonuclease/Exonuclease/phosphatase family 2 / Inositol polyphosphate phosphatase, catalytic domain homologues / SAM domain (Sterile alpha motif) / Endonuclease/exonuclease/phosphatase superfamily / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...SHIP1/2 second C2 domain / SHIP1/2 first C2 domain / Inositol polyphosphate-related phosphatase / Endonuclease/Exonuclease/phosphatase family 2 / Inositol polyphosphate phosphatase, catalytic domain homologues / 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
Similarity search - Domain/homology
Chem-D7I / Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsWhitfield, H. / Brearley, C.A. / Hemmings, A.M.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Allosteric Site on SHIP2 Identified Through Fluorescent Ligand Screening and Crystallography: A Potential New Target for Intervention.
Authors: Whitfield, H. / Hemmings, A.M. / Mills, S.J. / Baker, K. / White, G. / Rushworth, S. / Riley, A.M. / Potter, B.V.L. / Brearley, C.A.
History
DepositionSep 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2783
Polymers72,4882
Non-polymers7901
Water84747
1
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
2
B: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0342
Polymers36,2441
Non-polymers7901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.410, 60.190, 113.960
Angle α, β, γ (deg.)90.000, 92.750, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: 36243.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INPPL1, SHIP2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 pLysS
References: UniProt: O15357, phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase
#2: Chemical ChemComp-D7I / 5,5'-(ethane-1,2-diylbis(oxy))bis(benzene-5,4,2,1,-tetrayl)hexakisphosphate


Mass: 790.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20O26P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.17 M Ammonium sulfate, 25.5 % PEG 4000, 15 % glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.27→41.354 Å / Num. obs: 27911 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 49.57 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.05 / Rrim(I) all: 0.094 / Net I/σ(I): 9.6
Reflection shellResolution: 2.27→2.33 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.061 / Num. unique obs: 2067 / CC1/2: 0.538 / Rpim(I) all: 0.661 / Rrim(I) all: 1.253 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A9C

4a9c


Resolution: 2.27→41.35 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0.94 / Phase error: 28.67
RfactorNum. reflection% reflection
Rfree0.2537 1344 4.82 %
Rwork0.2008 --
obs0.2033 27891 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.56 Å2 / Biso mean: 66.2948 Å2 / Biso min: 29.08 Å2
Refinement stepCycle: final / Resolution: 2.27→41.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4688 0 54 47 4789
Biso mean--100.94 50.85 -
Num. residues----580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024855
X-RAY DIFFRACTIONf_angle_d0.5176596
X-RAY DIFFRACTIONf_chiral_restr0.043713
X-RAY DIFFRACTIONf_plane_restr0.002832
X-RAY DIFFRACTIONf_dihedral_angle_d13.782852
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.27-2.35110.35041340.29732636100
2.3511-2.44530.38261050.27622653100
2.4453-2.55650.30741320.26832642100
2.5565-2.69130.30771560.25272624100
2.6913-2.85990.32391310.23872644100
2.8599-3.08060.33241400.22192640100
3.0806-3.39050.28451580.2062264899
3.3905-3.88080.22571360.18322634100
3.8808-4.88820.21491320.1619268699
4.8882-41.350.20351200.1906274099
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)
13.8116-0.98160.20456.7707-4.08846.52070.10460.71180.5765-0.38280.28920.218-0.8264-0.5201-0.32710.6403-0.06350.01290.6080.22220.51491.768440.2346-50.1953
23.0968-0.93061.64234.8228-1.53872.29940.02390.23750.44020.17460.78010.9706-1.2509-1.8083-0.93970.62170.06870.12390.99080.40640.7787-9.567437.4527-37.5596
38.373-0.3093-0.46832.9799-0.59463.9627-0.0222-0.0375-0.22790.09430.41730.5623-0.19-0.6009-0.37040.3563-0.0191-0.00280.47340.21710.4504-0.606523.7115-31.1968
42.65652.16273.65177.130.42488.3803-0.54250.37010.08610.07690.3803-0.2061-0.3894-0.00220.09950.3253-0.08930.01740.54620.14250.53054.262829.7236-35.4056
56.8548-1.08190.10627.221-2.8720.8427-0.24871.58450.0669-0.71290.40350.171-0.03440.3313-0.22940.4965-0.1729-0.03120.72280.18180.41754.693229.983-45.1235
63.9909-1.89440.33884.2910.49314.4365-0.07450.2956-0.6807-0.40260.1260.69560.5777-0.3544-0.09390.4824-0.1831-0.01380.4040.04750.4798-18.9908-5.8424-14.2496
74.0070.92580.78346.60260.08133.75510.073-0.4289-0.66650.66850.11710.28790.6148-0.4556-0.17820.4627-0.07510.01630.39830.12840.3738-13.1233-6.7471-2.8603
89.4235-6.6892-0.64767.76732.68792.5662-0.1219-0.2843-0.3239-0.06530.18790.6676-0.0182-0.08940.05510.2605-0.0536-0.0220.370.09150.2551-9.15356.3803-9.0968
92.2626-7.97229.57372.3569-8.51372.368-0.4681-0.4910.98530.16710.2755-0.8025-0.3079-0.45680.27510.4756-0.0837-0.10270.53980.14610.6367-5.08515.514-7.1909
102.3317-1.7043-1.60467.86072.42924.63550.06910.17460.02540.60750.132-0.88480.22350.885-0.28540.4065-0.0370.03970.38950.03830.51580.63691.9162-5.6767
117.3421-0.09991.95794.8614-1.5614.1955-0.03250.63430.5521-0.3119-0.04380.12960.232-0.14640.05810.3222-0.0282-0.00090.44770.13770.3262-16.752412.8749-22.6429
120.41160.31380.60760.979-0.13651.03160.1082-0.00840.27810.13410.0131-0.0475-0.0614-0.0233-0.05330.3896-0.11420.02750.46810.09140.3337-16.428211.1353-15.5916
134.272-0.929-2.96025.89370.09475.0658-0.28830.5256-0.2438-0.1050.2796-0.05310.7941-0.3509-0.01820.4103-0.0847-0.09580.34930.02570.3312-15.532-2.652-17.8901
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 423 through 550 )A423 - 550
2X-RAY DIFFRACTION2chain 'A' and (resid 551 through 607 )A551 - 607
3X-RAY DIFFRACTION3chain 'A' and (resid 608 through 662 )A608 - 662
4X-RAY DIFFRACTION4chain 'A' and (resid 663 through 702 )A663 - 702
5X-RAY DIFFRACTION5chain 'A' and (resid 703 through 728 )A703 - 728
6X-RAY DIFFRACTION6chain 'B' and (resid 421 through 477 )B421 - 477
7X-RAY DIFFRACTION7chain 'B' and (resid 478 through 550 )B478 - 550
8X-RAY DIFFRACTION8chain 'B' and (resid 551 through 568 )B551 - 568
9X-RAY DIFFRACTION9chain 'B' and (resid 569 through 582 )B569 - 582
10X-RAY DIFFRACTION10chain 'B' and (resid 583 through 607 )B583 - 607
11X-RAY DIFFRACTION11chain 'B' and (resid 608 through 672 )B608 - 672
12X-RAY DIFFRACTION12chain 'B' and (resid 673 through 701 )B673 - 701
13X-RAY DIFFRACTION13chain 'B' and (resid 702 through 731 )B702 - 731

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