[English] 日本語
Yorodumi
- PDB-4cmn: Crystal structure of OCRL in complex with a phosphate ion -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cmn
TitleCrystal structure of OCRL in complex with a phosphate ion
ComponentsINOSITOL POLYPHOSPHATE 5-PHOSPHATASE OCRL-1
KeywordsHYDROLASE / INOSITOL SIGNALLING / SGC STOCKHOLM / STRUCTURAL GENOMICS CONSORTIUM / LOWE SYNDROME / DENT DISEASE
Function / homology
Function and homology information


phosphatidylinositol phosphate 4-phosphatase activity / inositol phosphate phosphatase activity / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / inositol-polyphosphate 5-phosphatase / inositol-1,3,4,5-tetrakisphosphate 5-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 ...phosphatidylinositol phosphate 4-phosphatase activity / inositol phosphate phosphatase activity / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / inositol-polyphosphate 5-phosphatase / inositol-1,3,4,5-tetrakisphosphate 5-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 / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation / Golgi stack / membrane organization / phosphatidylinositol biosynthetic process / clathrin-coated vesicle / Golgi-associated vesicle / Golgi Associated Vesicle Biogenesis / RHOJ GTPase cycle / Synthesis of IP3 and IP4 in the cytosol / Synthesis of PIPs at the plasma membrane / cilium assembly / photoreceptor outer segment / RAC3 GTPase cycle / clathrin-coated pit / GTPase activator activity / trans-Golgi network / lipid metabolic process / small GTPase binding / phagocytic vesicle membrane / Clathrin-mediated endocytosis / early endosome membrane / in utero embryonic development / lysosome / early endosome / signal transduction / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Inositol polyphosphate 5-phosphatase, clathrin binding domain / OCRL1, PH domain / Inositol polyphosphate 5-phosphatase clathrin binding domain / : / : / Inositol polyphosphate 5-phosphatase OCRL-like, ASH domain / OCRL1/INPP5B, INPP5c domain / : / Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues ...Inositol polyphosphate 5-phosphatase, clathrin binding domain / OCRL1, PH domain / Inositol polyphosphate 5-phosphatase clathrin binding domain / : / : / Inositol polyphosphate 5-phosphatase OCRL-like, ASH domain / OCRL1/INPP5B, INPP5c domain / : / Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Endonuclease/exonuclease/phosphatase superfamily / Rho GTPase activation protein / 4-Layer Sandwich / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Inositol polyphosphate 5-phosphatase OCRL
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsTresaugues, L. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Graslund, S. / Karlberg, T. ...Tresaugues, L. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Graslund, S. / Karlberg, T. / Nyman, T. / Schuler, H. / Silvander, C. / Thorsell, A.G. / Weigelt, J. / Welin, M. / Nordlund, P.
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
DepositionJan 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Dec 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_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INOSITOL POLYPHOSPHATE 5-PHOSPHATASE OCRL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8455
Polymers41,5421
Non-polymers3034
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)146.766, 146.766, 146.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

-
Components

#1: Protein INOSITOL POLYPHOSPHATE 5-PHOSPHATASE OCRL-1 / LOWE OCULOCEREBRORENAL SYNDROME PROTEIN / INOSITOL POLYPHOSPHATE 5-PHOSPHATASE OCRL-1 ISOFORM 1


Mass: 41541.617 Da / Num. of mol.: 1 / Fragment: 5-PHOSPHATASE CATALYTIC DOMAIN, RESIDUES 215-560 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION / Plasmid: PNIC-CH2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE / References: UniProt: Q01968, phosphoinositide 5-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAN ALANINE FOLLOWED BY A HEXAHISTIDINE TAG WAS ADDED TO THE C-TERMINUS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.74 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M ZINC ACETATE, 0.1 M NA-CACODYLATE PH 6.5, 10% ISOPROPANOL

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2011 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.13→103.78 Å / Num. obs: 10068 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 40.5 % / Biso Wilson estimate: 106.14 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.5
Reflection shellResolution: 3.13→3.3 Å / Redundancy: 42.4 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MTC

3mtc


Resolution: 3.13→48.922 Å / SU ML: 0.35 / σ(F): 1.96 / Phase error: 25.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2628 1003 10 %
Rwork0.2096 --
obs0.2151 10030 99.93 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.424 Å2 / ksol: 0.298 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.13→48.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2690 0 18 4 2712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062766
X-RAY DIFFRACTIONf_angle_d0.9973748
X-RAY DIFFRACTIONf_dihedral_angle_d15.241991
X-RAY DIFFRACTIONf_chiral_restr0.062406
X-RAY DIFFRACTIONf_plane_restr0.004487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1305-3.29550.3511380.24491260X-RAY DIFFRACTION100
3.2955-3.50190.28781110.21811277X-RAY DIFFRACTION100
3.5019-3.77220.28371440.21511266X-RAY DIFFRACTION100
3.7722-4.15160.26761380.20161270X-RAY DIFFRACTION100
4.1516-4.7520.21311490.16871267X-RAY DIFFRACTION100
4.752-5.98530.23251540.18561295X-RAY DIFFRACTION100
5.9853-48.9280.28881690.24021392X-RAY DIFFRACTION100
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)
13.1305-0.1065-1.35763.6415-1.78520.5317-0.02480.07780.14150.06060.29990.6658-0.0487-0.0135-0.10510.5804-0.20980.11581.2481-0.27460.5022-4.805135.3749-31.3425
22.9902-0.89810.56015.1587-0.42471.0741-0.3608-0.137-0.414-0.04071.0069-1.02770.36780.90660.07490.4028-0.22380.35811.5453-0.37750.7308-1.065532.9778-27.3381
33.39240.5525-2.0856.4146-1.32441.7297-0.0611-0.5303-0.96721.16340.8965-1.54750.87110.94070.39750.84780.3619-0.14251.8251-0.11690.93030.076331.0453-12.8437
44.5559-0.6204-1.5193.1484-1.47784.1484-0.13890.3631-0.20851.16790.54880.601-0.53050.1462-0.1810.53840.04010.361.1876-0.23350.7012-17.729138.8463-13.2044
52.1431-0.1115-0.96891.9134-1.14210.9994-0.04480.2391-0.22160.2950.45910.74030.1409-0.0007-0.16340.6324-0.11430.10431.3231-0.13780.8273-15.324639.061-24.059
60.13870.6906-0.70312.026-0.26555.3378-0.18050.5226-0.63910.09450.1946-1.61281.0041-0.67370.03330.3976-0.42610.70071.5783-0.1790.779528.208158.3513-33.8091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 217:306)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 307:379)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 380:411)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 412:480)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 481:541)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 542:559)

+
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