[English] 日本語
Yorodumi
- PDB-8pdh: The phosphatase and C2 domains of SHIP1 with covalent Z1742148362 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pdh
TitleThe phosphatase and C2 domains of SHIP1 with covalent Z1742148362
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
KeywordsHYDROLASE / ligand / phoshphatase / C2
Function / homology
Function and homology information


inositol-polyphosphate 5-phosphatase / negative regulation of neutrophil differentiation / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / inositol-1,4,5-trisphosphate 5-phosphatase activity / inositol-polyphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity ...inositol-polyphosphate 5-phosphatase / negative regulation of neutrophil differentiation / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / inositol-1,4,5-trisphosphate 5-phosphatase activity / inositol-polyphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / negative regulation of monocyte differentiation / phosphatidylinositol dephosphorylation / negative regulation of immune response / phosphatidylinositol biosynthetic process / phosphate-containing compound metabolic process / negative regulation of bone resorption / positive regulation of B cell differentiation / Synthesis of IP3 and IP4 in the cytosol / negative regulation of B cell proliferation / negative regulation of osteoclast differentiation / PECAM1 interactions / Synthesis of PIPs at the plasma membrane / negative regulation of interleukin-6 production / regulation of immune response / immunoglobulin mediated immune response / Interleukin receptor SHC signaling / negative regulation of signal transduction / positive regulation of erythrocyte differentiation / determination of adult lifespan / SH3 domain binding / Signaling by CSF1 (M-CSF) in myeloid cells / Downstream TCR signaling / T cell receptor signaling pathway / cytoskeleton / intracellular signal transduction / positive regulation of apoptotic process / membrane raft / apoptotic process / signal transduction / plasma membrane / cytosol
Similarity search - Function
Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / Endonuclease/exonuclease/phosphatase superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily
Similarity search - Domain/homology
(5-phenyl-1,3,4-oxadiazol-2-yl)methanimine / Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBradshaw, W.J. / Moreira, T. / Pascoa, T.C. / Bountra, C. / Chalk, R. / von Delft, F. / Brennan, P.E. / Gileadi, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA) United States
CitationJournal: Structure / Year: 2024
Title: Regulation of inositol 5-phosphatase activity by the C2 domain of SHIP1 and SHIP2.
Authors: Bradshaw, W.J. / Kennedy, E.C. / Moreira, T. / Smith, L.A. / Chalk, R. / Katis, V.L. / Benesch, J.L.P. / Brennan, P.E. / Murphy, E.J. / Gileadi, O.
History
DepositionJun 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3476
Polymers52,8781
Non-polymers4705
Water8,683482
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.508, 79.171, 89.378
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 / Inositol polyphosphate-5-phosphatase of 145 kDa / SIP-145 / SH2 domain-containing inositol 5'- ...Inositol polyphosphate-5-phosphatase of 145 kDa / SIP-145 / SH2 domain-containing inositol 5'-phosphatase 1 / SHIP-1 / p150Ship / hp51CN


Mass: 52877.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INPP5D, SHIP, SHIP1 / Plasmid: pFB-HGT-LIC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q92835, phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase, inositol-polyphosphate 5-phosphatase, phosphoinositide 5-phosphatase
#2: Chemical ChemComp-YBU / (5-phenyl-1,3,4-oxadiazol-2-yl)methanimine


Mass: 173.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulphate, 100 mM MES/imidazole, 20 % PEG 500 MME, 10% PEG 20,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→79.2 Å / Num. obs: 79287 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.998 / Net I/σ(I): 8
Reflection shellResolution: 1.45→1.47 Å / Num. unique obs: 3864 / CC1/2: 0.453 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→51.276 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.923 / SU ML: 0.062 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2018 2097 2.649 %
Rwork0.144 77079 -
all0.146 --
obs-79176 99.95 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.658 Å2
Baniso -1Baniso -2Baniso -3
1--0.088 Å20 Å20 Å2
2--0.478 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.45→51.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3704 0 29 482 4215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133977
X-RAY DIFFRACTIONr_bond_other_d0.0030.0153714
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.6465419
X-RAY DIFFRACTIONr_angle_other_deg1.4551.5768621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3755505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15723.415205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71315712
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg8.335151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9611517
X-RAY DIFFRACTIONr_chiral_restr0.0920.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024507
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02914
X-RAY DIFFRACTIONr_nbd_refined0.2380.2701
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.23493
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21839
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21933
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2357
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1020.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2130.229
X-RAY DIFFRACTIONr_nbd_other0.2280.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2110.232
X-RAY DIFFRACTIONr_mcbond_it3.8411.8651887
X-RAY DIFFRACTIONr_mcbond_other3.841.8631886
X-RAY DIFFRACTIONr_mcangle_it4.9032.8132369
X-RAY DIFFRACTIONr_mcangle_other4.9022.8142370
X-RAY DIFFRACTIONr_scbond_it4.362.2232090
X-RAY DIFFRACTIONr_scbond_other4.3592.2232091
X-RAY DIFFRACTIONr_scangle_it5.5433.183026
X-RAY DIFFRACTIONr_scangle_other5.5423.183027
X-RAY DIFFRACTIONr_lrange_it6.01722.8324502
X-RAY DIFFRACTIONr_lrange_other5.86622.2384390
X-RAY DIFFRACTIONr_rigid_bond_restr3.08937691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.4880.2971380.285648X-RAY DIFFRACTION99.9137
1.488-1.5280.2831600.2645488X-RAY DIFFRACTION99.9469
1.528-1.5730.271480.2275327X-RAY DIFFRACTION99.9452
1.573-1.6210.2441200.1975205X-RAY DIFFRACTION99.9437
1.621-1.6740.271370.195019X-RAY DIFFRACTION99.8644
1.674-1.7330.231400.1744891X-RAY DIFFRACTION99.9603
1.733-1.7980.2281260.1544713X-RAY DIFFRACTION99.8968
1.798-1.8720.2791290.1484535X-RAY DIFFRACTION99.9357
1.872-1.9550.2491260.1394349X-RAY DIFFRACTION99.9777
1.955-2.050.1991160.1244163X-RAY DIFFRACTION99.9766
2.05-2.1610.1641040.1143990X-RAY DIFFRACTION99.9512
2.161-2.2920.1621130.1083771X-RAY DIFFRACTION100
2.292-2.450.182910.1073538X-RAY DIFFRACTION99.9449
2.45-2.6450.187880.1153342X-RAY DIFFRACTION100
2.645-2.8970.191850.1123045X-RAY DIFFRACTION99.9681
2.897-3.2380.191680.1332792X-RAY DIFFRACTION99.965
3.238-3.7380.19660.1292498X-RAY DIFFRACTION100
3.738-4.5730.128640.1052101X-RAY DIFFRACTION100
4.573-6.4480.195450.1731681X-RAY DIFFRACTION100
6.448-51.2760.234330.232984X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more