[English] 日本語
Yorodumi
- PDB-6xy7: Human SHIP1 with magnesium and phosphate bound to the active site -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xy7
TitleHuman SHIP1 with magnesium and phosphate bound to the active site
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
KeywordsHYDROLASE / Phosphatidylinositol / phosphate / phosphatase / Alzheimer's Disease
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 3-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / inositol-1,4,5-trisphosphate 5-phosphatase activity / inositol-polyphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / 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 3-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / inositol-1,4,5-trisphosphate 5-phosphatase activity / inositol-polyphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / 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 / immunoglobulin mediated immune response / regulation of 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 family / 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
TRIETHYLENE GLYCOL / PHOSPHATE ION / Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.086 Å
AuthorsBradshaw, W.J. / Scacioc, A. / Fernandez-Cid, A. / Mckinley, G. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gileadi, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1U54AG065187-01 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
DepositionJan 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Feb 14, 2024Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
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)53,3817
Polymers52,8781
Non-polymers5046
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-2 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.500, 79.088, 89.255
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules AAA

#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 / 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

-
Non-polymers , 5 types, 495 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O

-
Details

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: 41.03 %
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, pH 6.5, 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: 0.8266 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.086→59.193 Å / Num. obs: 159826 / % possible obs: 87.6 % / Redundancy: 26.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.03 / Rrim(I) all: 0.155 / Net I/σ(I): 11.7
Reflection shellResolution: 1.093→1.14 Å / Redundancy: 20.7 % / Rmerge(I) obs: 2.19 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7907 / CC1/2: 0.601 / Rpim(I) all: 0.48 / Rrim(I) all: 2.246 / % possible all: 59.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OKM

5okm


Resolution: 1.086→59.193 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.277 / SU ML: 0.026 / Cross valid method: FREE R-VALUE / ESU R: 0.031 / ESU R Free: 0.031
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1587 1775 1.111 %
Rwork0.1358 --
all0.136 --
obs-159810 85.905 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.339 Å2
Baniso -1Baniso -2Baniso -3
1-0.079 Å2-0 Å20 Å2
2---0.008 Å2-0 Å2
3----0.071 Å2
Refinement stepCycle: LAST / Resolution: 1.086→59.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3704 0 28 489 4221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134345
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174029
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.6495976
X-RAY DIFFRACTIONr_angle_other_deg1.4651.5739508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4425594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75423.277235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71115830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.4581522
X-RAY DIFFRACTIONr_chiral_restr0.0910.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024928
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02914
X-RAY DIFFRACTIONr_nbd_refined0.2130.2749
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.23709
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21911
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21921
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2377
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2230.239
X-RAY DIFFRACTIONr_nbd_other0.2220.2112
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.238
X-RAY DIFFRACTIONr_mcbond_it1.8891.2922014
X-RAY DIFFRACTIONr_mcbond_other1.8811.292013
X-RAY DIFFRACTIONr_mcangle_it2.4811.9442554
X-RAY DIFFRACTIONr_mcangle_other2.4831.9462555
X-RAY DIFFRACTIONr_scbond_it2.1271.5352331
X-RAY DIFFRACTIONr_scbond_other2.1271.5352332
X-RAY DIFFRACTIONr_scangle_it2.7092.2053356
X-RAY DIFFRACTIONr_scangle_other2.7082.2053357
X-RAY DIFFRACTIONr_lrange_it3.41616.054896
X-RAY DIFFRACTIONr_lrange_other3.28315.4814780
X-RAY DIFFRACTIONr_rigid_bond_restr1.90138374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.093-1.1150.233140.2631789X-RAY DIFFRACTION13.203
1.115-1.1450.251810.2397481X-RAY DIFFRACTION56.9085
1.145-1.1780.197960.2049625X-RAY DIFFRACTION75.4092
1.178-1.2150.1951080.17910649X-RAY DIFFRACTION85.5495
1.215-1.2540.1941250.17510832X-RAY DIFFRACTION89.9073
1.254-1.2980.1951140.16310877X-RAY DIFFRACTION93.1599
1.298-1.3470.151180.15310906X-RAY DIFFRACTION96.8802
1.347-1.4020.2081350.14510574X-RAY DIFFRACTION97.603
1.402-1.4650.1581220.12910212X-RAY DIFFRACTION97.8228
1.465-1.5360.2261090.1499761X-RAY DIFFRACTION98.2676
1.536-1.6190.121180.1359326X-RAY DIFFRACTION98.3853
1.619-1.7170.136960.1038869X-RAY DIFFRACTION98.6357
1.717-1.8360.138930.0988409X-RAY DIFFRACTION98.941
1.836-1.9830.117960.17817X-RAY DIFFRACTION99.0735
1.983-2.1720.107690.1057254X-RAY DIFFRACTION99.4162
2.172-2.4270.149900.1096572X-RAY DIFFRACTION99.4774
2.427-2.8020.152710.125860X-RAY DIFFRACTION99.731
2.802-3.430.139560.1364993X-RAY DIFFRACTION99.8615
3.43-4.8430.186390.1383935X-RAY DIFFRACTION99.9748
4.843-59.1930.216250.2112295X-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://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