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- PDB-2kie: A PH domain within OCRL bridges clathrin mediated membrane traffi... -

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Basic information

Entry
Database: PDB / ID: 2kie
TitleA PH domain within OCRL bridges clathrin mediated membrane trafficking to phosphoinositide metabolis
ComponentsInositol polyphosphate 5-phosphatase OCRL-1
KeywordsHYDROLASE / OCRL / INPP5B / PH / clathrin / endocytosis / Alternative splicing / Cataract / Disease mutation
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 / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / Synthesis of PIPs at the Golgi membrane / 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
PH-domain like - #110 / 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 ...PH-domain like - #110 / 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 / 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 like / Roll / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Inositol polyphosphate 5-phosphatase OCRL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMao, Y. / Balkin, D.M. / Zoncu, R. / Erdmann, K. / Tomasini, L. / Hu, F. / Jin, M.M. / Hodsdon, M.E. / De Camilli, P.
CitationJournal: Embo J. / Year: 2009
Title: A PH domain within OCRL bridges clathrin-mediated membrane trafficking to phosphoinositide metabolism
Authors: Mao, Y. / Balkin, D.M. / Zoncu, R. / Erdmann, K.S. / Tomasini, L. / Hu, F. / Jin, M.M. / Hodsdon, M.E. / De Camilli, P.
History
DepositionMay 3, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _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)13,8701
Polymers13,8701
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 13869.876 Da / Num. of mol.: 1 / Fragment: N-terminal residues 1-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OCRL, INPP5F, OCRL1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q01968, phosphoinositide 5-phosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CA)CB
1513D HN(CO)CA
1613D CBCA(CO)NH
1713D C(CO)NH
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] protein , 20 mM potassium phosphate
Solvent system: 90% H2O/10% D2O
SampleConc.: 20 mM / Component: potassium phosphate-1
Sample conditionspH: 6.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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