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- PDB-4a9c: Crystal structure of human SHIP2 in complex with biphenyl 2,3',4,... -

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Basic information

Entry
Database: PDB / ID: 4a9c
TitleCrystal structure of human SHIP2 in complex with biphenyl 2,3',4,5',6- pentakisphosphate
ComponentsPHOSPHATIDYLINOSITOL-3,4,5-TRISPHOSPHATE 5-PHOSPHATASE 2
KeywordsHYDROLASE / SGC / PHOSPHATIDYLINOSITOL / SIGNALLING / STRUCTURAL GENOMICS CONSORTIUM STOCKHOLM / MAGNESIUM BINDING / INHIBITOR
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
BIPHENYL 2,3',4,5',6-PENTAKISPHOSPHATE / Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Ekblad, T. / Graslund, S. / Karlberg, T. / Mills, S.J. / Moche, M. ...Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Ekblad, T. / Graslund, S. / Karlberg, T. / Mills, S.J. / Moche, M. / Nyman, T. / Persson, C. / Potter, B.V.L. / Schuler, H. / Thorsell, A.G. / Weigelt, J. / Nordlund, P.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: A Synthetic Polyphosphoinositide Headgroup Surrogate in Complex with Ship2 Provides a Rationale for Drug Discovery.
Authors: Mills, S.J. / Persson, C. / Cozier, G. / Thomas, M.P. / Tresaugues, L. / Erneux, C. / Riley, A.M. / Nordlund, P. / Potter, B.V.L.
History
DepositionNov 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 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-3,4,5-TRISPHOSPHATE 5-PHOSPHATASE 2
B: PHOSPHATIDYLINOSITOL-3,4,5-TRISPHOSPHATE 5-PHOSPHATASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1223
Polymers72,4882
Non-polymers6341
Water4,540252
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
MethodPISA
2
B: PHOSPHATIDYLINOSITOL-3,4,5-TRISPHOSPHATE 5-PHOSPHATASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8782
Polymers36,2441
Non-polymers6341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.246, 61.520, 114.742
Angle α, β, γ (deg.)90.00, 91.94, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.991, 0.107, -0.074), (0.072, -0.023, -0.997), (-0.108, -0.994, 0.015)
Vector: -32.911, -39.273, 17.713)

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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 / SH2 DOMAIN-CONTAINING INOSITOL PHOSPHATASE 2 / SHIP-2


Mass: 36243.852 Da / Num. of mol.: 2 / Fragment: PHOSPHATASE DOMAIN, RESIDUES 419-732
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-MBP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE
References: UniProt: O15357, phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase
#2: Chemical ChemComp-B5F / BIPHENYL 2,3',4,5',6-PENTAKISPHOSPHATE


Mass: 634.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15O20P5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.2 Å3/Da / Density % sol: 44.14 % / Description: NONE
Crystal growpH: 4.8
Details: 1.5 MM BIPHENYL 2,3,4,5, 6-PENTAKISPHOSPHATE, 2 MM MGSO4, 11% PEG 6000, 0.1 M CITRIC ACID PH 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93928
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93928 Å / Relative weight: 1
ReflectionResolution: 2.1→45.22 Å / Num. obs: 36559 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 37.61 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.2 / % possible all: 98.4

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NR8

3nr8


Resolution: 2.1→29.41 Å / Cor.coef. Fo:Fc: 0.9395 / Cor.coef. Fo:Fc free: 0.9335 / SU R Cruickshank DPI: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.232 / SU Rfree Blow DPI: 0.17 / SU Rfree Cruickshank DPI: 0.172
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1787 4.89 %RANDOM
Rwork0.2009 ---
obs0.2019 36540 98.74 %-
Displacement parametersBiso mean: 46.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.2514 Å20 Å22.9253 Å2
2--5.0585 Å20 Å2
3---0.8071 Å2
Refine analyzeLuzzati coordinate error obs: 0.361 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4686 0 37 252 4975
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084863HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.96614HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2206SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes109HARMONIC2
X-RAY DIFFRACTIONt_gen_planes702HARMONIC5
X-RAY DIFFRACTIONt_it4863HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.36
X-RAY DIFFRACTIONt_other_torsion2.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion624SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5711SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2641 145 4.88 %
Rwork0.2285 2825 -
all0.2302 2970 -
obs--98.74 %
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)
12.20830.50230.28595.65612.57984.1922-0.0367-0.22930.14870.16180.2846-0.1288-0.28-0.0725-0.2479-0.05590.03910.0334-0.1717-0.0732-0.0989-22.53929.1345-6.8035
21.1051-0.4221-2.56682.85480.0781-0.1752-0.03440.01630.1495-0.04610.1351-0.28040.02830.0575-0.10070.0184-0.1350.1288-0.0834-0.1469-0.0025-13.33687.5451-17.87
30.43342.582-0.9280-0.41540.622-0.0198-0.0060.01870.04430.0192-0.08740.00590.01650.0006-0.0042-0.14750.1495-0.0096-0.14130.0818-6.885410.6235-22.9896
40.1196-1.5205-1.07012.00531.85290.13530.00830.08030.0776-0.01740.1436-0.1574-0.048-0.0713-0.1518-0.0198-0.12750.1024-0.0292-0.0642-0.0056-18.0507-1.0171-23.9347
54.136-0.2198-0.02753.86522.71185.7278-0.00730.2041-0.0365-0.15790.2426-0.1743-0.08560.044-0.2353-0.1034-0.06990.065-0.1094-0.0857-0.0848-21.8989-4.2117-24.2997
60.50830.77260.16692.80270.84893.6577-0.0055-0.05860.03510.14010.1236-0.2040.07780.0914-0.11810.04450.02850.0185-0.0947-0.08-0.0175-18.4286-1.3459-9.6091
70.0744-0.75970.45072.01171.0541.6447-0.00050.0448-0.22160.1243-0.02470.0120.2620.08670.0253-0.17070.0360.00130.2492-0.1511-0.1008-1.436224.8201-42.7464
80.5032-0.5060.13591.95191.89542.17930.01310.1815-0.1207-0.09340.02560.0050.19660.0543-0.0387-0.22750.0530.01320.2794-0.1509-0.1266-5.780523.9849-54.5916
90.8912-0.9238-0.34360.5712-0.29412.47290.02290.31560.0002-0.0977-0.05730.05510.00230.00380.0344-0.2118-0.01680.01580.2829-0.1521-0.1146-13.745938.6543-50.2149
103.6848-0.2274-0.37582.01441.20131.12010.0408-0.0290.0860.1698-0.0633-0.01250.09330.11770.0225-0.1347-0.07010.04650.1434-0.1272-0.1141-6.271141.7847-37.5322
110.46710.24120.44240.2965-0.25360.2871-0.0069-0.00090.0713-0.0284-0.02210.0359-0.0231-0.00810.029-0.0124-0.02180.04040.1358-0.0426-0.015310.38851.6878-44.6941
120.1132-0.3336-1.23112.59740.28621.5352-0.0036-0.0523-0.1140.1174-0.00160.12650.2315-0.0510.0052-0.1358-0.0581-0.00790.151-0.1541-0.112-8.435730.7347-39.5013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 422-547
2X-RAY DIFFRACTION2CHAIN A AND RESID 548-571
3X-RAY DIFFRACTION3CHAIN A AND RESID 572-596
4X-RAY DIFFRACTION4CHAIN A AND RESID 597-622
5X-RAY DIFFRACTION5CHAIN A AND RESID 623-696
6X-RAY DIFFRACTION6CHAIN A AND RESID 697-731
7X-RAY DIFFRACTION7CHAIN B AND RESID 422-472
8X-RAY DIFFRACTION8CHAIN B AND RESID 473-544
9X-RAY DIFFRACTION9CHAIN B AND RESID 545-584
10X-RAY DIFFRACTION10CHAIN B AND RESID 585-671
11X-RAY DIFFRACTION11CHAIN B AND RESID 672-685
12X-RAY DIFFRACTION12CHAIN B AND RESID 686-731

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