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- PDB-2qv2: A role of the Lowe syndrome protein OCRL in early steps of the en... -

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Basic information

Entry
Database: PDB / ID: 2qv2
TitleA role of the Lowe syndrome protein OCRL in early steps of the endocytic pathway
ComponentsInositol polyphosphate 5-phosphatase OCRL-1
KeywordsHYDROLASE / endocytosis / clathrin / APPL1 / phosphoinositide / ASH / RhoGAP
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 / : / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein ...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 / : / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Inositol polyphosphate 5-phosphatase OCRL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsMao, Y. / Erdman, K.S. / McCrea, H.J. / De Camilli, P.
CitationJournal: Dev.Cell / Year: 2007
Title: A role of the Lowe syndrome protein OCRL in early steps of the endocytic pathway
Authors: Erdmann, K.S. / Mao, Y. / McCrea, H.J. / Zoncu, R. / Lee, S. / Paradise, S. / Modregger, J. / Biemesderfer, D. / Toomre, D. / De Camilli, P.
History
DepositionAug 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inositol polyphosphate 5-phosphatase OCRL-1


Theoretical massNumber of molelcules
Total (without water)39,4701
Polymers39,4701
Non-polymers00
Water75742
1
A: Inositol polyphosphate 5-phosphatase OCRL-1

A: Inositol polyphosphate 5-phosphatase OCRL-1


Theoretical massNumber of molelcules
Total (without water)78,9402
Polymers78,9402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area33228 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.300, 91.300, 103.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Inositol polyphosphate 5-phosphatase OCRL-1 / E.C.3.1.3.36 / OCRL / Lowe oculocerebrorenal syndrome protein


Mass: 39470.227 Da / Num. of mol.: 1 / Fragment: ASH-RhoGAP-like tandem domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OCRL, INPP5F, OCRL1 / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q01968, phosphoinositide 5-phosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.17 Å3/Da / Density % sol: 61.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Hepes, 8.5% PEG8000, 400 mM NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793, 0.9840
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2005
RadiationMonochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.9841
ReflectionResolution: 2.4→43.42 Å / Num. all: 20485 / Num. obs: 18866 / % possible obs: 94.3 % / Observed criterion σ(I): 1 / Redundancy: 11.3 % / Biso Wilson estimate: 47.3 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 43.9

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→43.42 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 813 -RANDOM
Rwork0.248 ---
all0.2481 20006 --
obs-18866 94.3 %-
Refine analyzeLuzzati coordinate error obs: 0.37 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.4→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 0 42 2531
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0073
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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