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2qv2

A role of the Lowe syndrome protein OCRL in early steps of the endocytic pathway

Method: X-RAY DIFFRACTION Dmax: 81.9 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 564–901 Fragment：ASH-RhoGAP-like tandem domains No other associated polymer 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

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 2QV2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2KIE A PH domain within OCRL bridges clathrin mediated membrane trafficking to phosphoinositide metabolis Deposited 2009-05-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–119（119 aa） Fragment：N-terminal residues 1-119
Not recorded No recorded non-water small molecule 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
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 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 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 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 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 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 oligomeric state Different ligand/ion 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 5–342； UniProt 564–901

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 2qv2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2qv2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2qv2
Deposition date deposition_date2007-08-07
Structure title titleA role of the Lowe syndrome protein OCRL in early steps of the endocytic pathway
Keywords keywordsendocytosis, clathrin, APPL1, phosphoinositide, ASH, RhoGAP, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.80 Å
Radius of gyration Rg (electron density) rg_electron23.90 Å
Forward intensity I(0) i020503100.00
Molecular weight molecular_weight35392.0 kDa
Excluded volume excluded_volume44760 ų
Envelope volume envelope_volume59007 ų
Hydration-shell volume shell_volume21692 ų
Envelope diameter envelope_diameter84.9 Å
Shell Rg shell_rg29.54 Å
Envelope Rg envelope_rg24.63 Å
Shape Rg shape_rg23.92 Å
Total Rg total_rg24.60 Å
Total atoms total_atoms2489
Residues n_residues305
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 dmax81.9 Å
Rg (real space) rg_real24.85 Å
Rg uncertainty (real space) rg_real_error0.77 Å
I(0) (real space) i0_real2.0500e+07
I(0) uncertainty (real space) i0_real_error2.9140e+05
Rg (reciprocal space) rg_reciprocal24.84 Å
I(0) (reciprocal space) i0_reciprocal20500000.0000
Solution quality estimate total_estimate0.8169
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.6 Å
Skewness Skewness skewness0.335
Kurtosis Kurtosis kurtosis-0.481
Angular range angular_range— – 0.3200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2459000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id2qv2A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2qv2A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology555 — Phosphatidylinositol 3-kinase; Chain A
Homologous superfamily homologous superfamily10 — Rho GTPase activation protein
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8. Citations (1)

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9. Files and Curves (10)