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- PDB-3qis: Recognition of the F&H motif by the Lowe Syndrome protein OCRL -

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Basic information

Entry
Database: PDB / ID: 3qis
TitleRecognition of the F&H motif by the Lowe Syndrome protein OCRL
Components
  • Inositol polyphosphate 5-phosphatase OCRL-1
  • Protein FAM109A
KeywordsHYDROLASE/PROTEIN BINDING / Dent Disease / Rac1 / Rab GTPases / APPL1 / Ses2 / Endocytic pathway / Golgi complex / HYDROLASE-PROTEIN BINDING complex
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 / receptor recycling / inositol-polyphosphate 5-phosphatase / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / 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 / receptor recycling / inositol-polyphosphate 5-phosphatase / 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 / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / endosome organization / phosphatidylinositol dephosphorylation / Golgi stack / membrane organization / phosphatidylinositol biosynthetic process / retrograde transport, endosome to Golgi / 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 / photoreceptor outer segment / cilium assembly / RAC3 GTPase cycle / clathrin-coated pit / GTPase activator activity / trans-Golgi network / lipid metabolic process / recycling endosome / small GTPase binding / phagocytic vesicle membrane / Clathrin-mediated endocytosis / early endosome membrane / in utero embryonic development / lysosome / early endosome / signal transduction / protein homodimerization activity / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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 / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Inositol polyphosphate 5-phosphatase OCRL / Sesquipedalian-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsPirruccello, M. / Swan, L.E. / Folta-Stogniew, E. / De Camilli, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Recognition of the F&H motif by the Lowe syndrome protein OCRL.
Authors: Pirruccello, M. / Swan, L.E. / Folta-Stogniew, E. / De Camilli, P.
History
DepositionJan 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol polyphosphate 5-phosphatase OCRL-1
B: Protein FAM109A


Theoretical massNumber of molelcules
Total (without water)44,2442
Polymers44,2442
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-10 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.478, 73.478, 145.294
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Inositol polyphosphate 5-phosphatase OCRL-1 / Lowe oculocerebrorenal syndrome protein


Mass: 42678.895 Da / Num. of mol.: 1 / Fragment: ASH-RhoGAP (UNP residues 536-901)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INPP5F, OCRL, OCRL1 / Plasmid: pGEX6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01968, phosphoinositide 5-phosphatase
#2: Protein/peptide Protein FAM109A / Ses1


Mass: 1564.763 Da / Num. of mol.: 1 / Fragment: F&H Motif (UNP residues 223-235) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8N4B1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 1.7 M ammonium sulfate, 0.1 M MES, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→63.634 Å / Num. all: 20848 / Num. obs: 20465 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 2.5 / % possible all: 93.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QV2

2qv2


Resolution: 2.3→24.051 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.27 / σ(F): 0 / Phase error: 22.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1012 5.13 %RANDOM
Rwork0.1954 ---
obs0.1975 19735 94.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.937 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 263.76 Å2 / Biso mean: 48.595 Å2 / Biso min: 15.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.056 Å20 Å20 Å2
2---0.056 Å2-0 Å2
3---0.1121 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 0 123 2631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062567
X-RAY DIFFRACTIONf_angle_d0.93473
X-RAY DIFFRACTIONf_chiral_restr0.058382
X-RAY DIFFRACTIONf_plane_restr0.003449
X-RAY DIFFRACTIONf_dihedral_angle_d15.199977
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.42120.30391370.24852568270593
2.4212-2.57270.33661480.23122637278596
2.5727-2.77110.27861440.22482687283196
2.7711-3.04950.27261710.2162697286897
3.0495-3.48960.24561460.19952747289398
3.4896-4.39220.22591370.18152390252784
4.3922-24.05260.17541290.17012997312699
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)
11.5152-0.23440.22070.93230.19031.855-0.141-0.06740.22640.29630.1167-0.2932-0.12260.12760.06770.34720.0702-0.12740.1634-0.05610.2619-40.427836.913541.7626
21.5378-0.70770.52923.05752.12352.204-0.2365-0.03680.04070.7873-0.02240.06570.36360.14020.19380.41950.0959-0.07510.175-0.00890.1279-36.914320.046841.0033
31.05510.0889-0.33261.04921.22441.6178-0.08870.0044-0.02760.21190.01430.050.0050.01480.08910.26640.1052-0.03760.1062-0.00820.1689-41.35119.412322.7543
40.51290.7824-0.3631.70150.46495.4362-0.02390.2463-0.0205-0.04530.0847-0.3902-0.16151.256-0.08920.23180.02870.00270.4612-0.0050.2919-23.610110.215615.4158
50.39311.24460.34074.34651.58673.5530.16680.1132-0.2633-0.09320.5041-0.7771-0.0750.1249-0.44430.19850.1186-0.00250.2524-0.08980.2488-34.3547-4.749216.9508
65.7992-5.6242-0.97217.19270.78850.55-0.7868-0.5094-0.53191.41471.01270.6654-0.15860.3616-0.29690.62790.3923-0.06130.46830.02220.331-34.9103-5.520226.7492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 563:661)A563 - 661
2X-RAY DIFFRACTION2(chain A and resid 662:696)A662 - 696
3X-RAY DIFFRACTION3(chain A and resid 730:800)A730 - 800
4X-RAY DIFFRACTION4(chain A and resid 801:896)A801 - 896
5X-RAY DIFFRACTION5(chain B and resid 1:7)B1 - 7
6X-RAY DIFFRACTION6(chain B and resid 8:13)B8 - 13

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