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2kie

A PH domain within OCRL bridges clathrin mediated membrane trafficking to phosphoinositide metabolis

Method: SOLUTION NMR Dmax: 48.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Inositol polyphosphate 5-phosphatase OCRL-1

Homo sapiens

UniProt Q01968

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–119 Fragment：N-terminal residues 1-119 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.4；298 K；Pressure ambient NMR sample composition：1 mM [U-100% 13C; U-100% 15N] protein , 20 mM potassium phosphate | 90% H2O/10% D2O Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2KIE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2QV2 A role of the Lowe syndrome protein OCRL in early steps of the endocytic pathway Deposited 2007-08-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 564–901（338 aa） Fragment：ASH-RhoGAP-like tandem domains
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM Hepes, 8.5% PEG8000, 400 mM NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.288
3QBT Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp Deposited 2011-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 540–678（139 aa） Fragment：unp residues 540-678
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K
Resolution 2.00 Å R-free 0.241
3QBT Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp Deposited 2011-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 540–678（139 aa） Fragment：unp residues 540-678
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K
Resolution 2.00 Å R-free 0.241
3QBT Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp Deposited 2011-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 540–678（139 aa） Fragment：unp residues 540-678
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K
Resolution 2.00 Å R-free 0.241
3QBT Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp Deposited 2011-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 540–678（139 aa） Fragment：unp residues 540-678
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K
Resolution 2.00 Å R-free 0.241
3QIS Recognition of the F&H motif by the Lowe Syndrome protein OCRL Deposited 2011-01-27 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 536–901（366 aa） Fragment：ASH-RhoGAP (UNP residues 536-901)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；1.7 M ammonium sulfate, 0.1 M MES, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.30 Å R-free 0.238
4CMN Crystal structure of OCRL in complex with a phosphate ion Deposited 2014-01-16 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 215–560（346 aa） Fragment：5-PHOSPHATASE CATALYTIC DOMAIN, RESIDUES 215-560
Mutation：YES PO4 PHOSPHATE ION × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.2 M ZINC ACETATE, 0.1 M NA-CACODYLATE PH 6.5, 10% ISOPROPANOL
Resolution 3.13 Å R-free 0.263

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OCRL_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–124； UniProt 1–119

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2kie

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2kie
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2kie
Deposition date deposition_date2009-05-03
Structure title titleA PH domain within OCRL bridges clathrin mediated membrane trafficking to phosphoinositide metabolis
Keywords keywordsOCRL, INPP5B, PH, clathrin, endocytosis, Alternative splicing, Cataract, Disease mutation, Hydrolase; HYDROLASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.37 Å
Radius of gyration Rg (electron density) rg_electron14.06 Å
Forward intensity I(0) i01107120000.00
Molecular weight molecular_weight276960.0 kDa
Excluded volume excluded_volume344800 ų
Envelope volume envelope_volume32962 ų
Hydration-shell volume shell_volume16617 ų
Envelope diameter envelope_diameter54.3 Å
Shell Rg shell_rg22.90 Å
Envelope Rg envelope_rg17.06 Å
Shape Rg shape_rg14.04 Å
Total Rg total_rg14.27 Å
Total atoms total_atoms38800
Residues n_residues2480
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax48.6 Å
Rg (real space) rg_real14.28 Å
Rg uncertainty (real space) rg_real_error0.33 Å
I(0) (real space) i0_real1.1070e+09
I(0) uncertainty (real space) i0_real_error1.1970e+07
Rg (reciprocal space) rg_reciprocal14.29 Å
I(0) (reciprocal space) i0_reciprocal1107000000.0000
Solution quality estimate total_estimate0.8561
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.7 Å
Skewness Skewness skewness0.111
Kurtosis Kurtosis kurtosis-0.277
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha421700.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.714; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.985
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2kieA00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily110 —
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8. Citations (1)

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9. Files and Curves (10)