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- PDB-3qbt: Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp -

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Basic information

Entry
Database: PDB / ID: 3qbt
TitleCrystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp
Components
  • Inositol polyphosphate 5-phosphatase OCRL-1
  • Ras-related protein Rab-8A
KeywordsPROTEIN TRANSPORT/HYDROLASE / Protein transport / vesicular trafficking / GTPase / Lowe syndrome / immunoglobulin fold / Rab8a / OCRL1 / endocytosis / clathrin / APPL1 / phosphoinositide / ASH / RhoGAP / PROTEIN TRANSPORT-HYDROLASE complex
Function / homology
Function and homology information


phosphatidylinositol phosphate 4-phosphatase activity / inositol phosphate phosphatase activity / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / Synthesis of IP2, IP, and Ins in the cytosol / vesicle-mediated transport in synapse / regulation of protein transport / inositol phosphate metabolic process / inositol-polyphosphate 5-phosphatase ...phosphatidylinositol phosphate 4-phosphatase activity / inositol phosphate phosphatase activity / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / Synthesis of IP2, IP, and Ins in the cytosol / vesicle-mediated transport in synapse / regulation of protein transport / inositol phosphate metabolic process / inositol-polyphosphate 5-phosphatase / VxPx cargo-targeting to cilium / 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 / neurotransmitter receptor transport, endosome to postsynaptic membrane / phosphoinositide 5-phosphatase / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol dephosphorylation / Golgi stack / RAB geranylgeranylation / myosin V binding / vesicle docking involved in exocytosis / membrane organization / regulation of exocytosis / trans-Golgi network transport vesicle / protein localization to cilium / RAB GEFs exchange GTP for GDP on RABs / phosphatidylinositol biosynthetic process / non-motile cilium / endocytic recycling / TBC/RABGAPs / ciliary membrane / clathrin-coated vesicle / ciliary base / Golgi-associated vesicle / Golgi Associated Vesicle Biogenesis / RHOJ GTPase cycle / Golgi organization / Synthesis of IP3 and IP4 in the cytosol / Synthesis of PIPs at the plasma membrane / protein secretion / cilium assembly / photoreceptor outer segment / RAC3 GTPase cycle / phagocytic vesicle / clathrin-coated pit / protein tyrosine kinase binding / Anchoring of the basal body to the plasma membrane / centriole / GTPase activator activity / axonogenesis / small monomeric GTPase / trans-Golgi network membrane / ciliary basal body / regulation of autophagy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to plasma membrane / regulation of long-term neuronal synaptic plasticity / trans-Golgi network / lipid metabolic process / cilium / small GTPase binding / autophagy / cellular response to insulin stimulus / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / Regulation of PLK1 Activity at G2/M Transition / synaptic vesicle / Clathrin-mediated endocytosis / midbody / early endosome membrane / in utero embryonic development / dendritic spine / postsynaptic density / lysosome / early endosome / endosome membrane / endosome / Golgi membrane / GTPase activity / centrosome / neuronal cell body / glutamatergic synapse / GTP binding / signal transduction / extracellular exosome / 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 / : / Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues ...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 / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / small GTPase Rab1 family profile. / Endonuclease/exonuclease/phosphatase superfamily / Rho GTPase activation protein / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-8A / Inositol polyphosphate 5-phosphatase OCRL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHou, X. / Hagemann, N. / Schoebel, S. / Blankenfeldt, W. / Goody, R.S. / Erdmann, K.S. / Itzen, A.
CitationJournal: Embo J. / Year: 2011
Title: A structural basis for Lowe syndrome caused by mutations in the Rab-binding domain of OCRL1.
Authors: Hou, X. / Hagemann, N. / Schoebel, S. / Blankenfeldt, W. / Goody, R.S. / Erdmann, K.S. / Itzen, A.
History
DepositionJan 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-8A
C: Ras-related protein Rab-8A
E: Ras-related protein Rab-8A
G: Ras-related protein Rab-8A
B: Inositol polyphosphate 5-phosphatase OCRL-1
D: Inositol polyphosphate 5-phosphatase OCRL-1
F: Inositol polyphosphate 5-phosphatase OCRL-1
H: Inositol polyphosphate 5-phosphatase OCRL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,64518
Polymers146,2678
Non-polymers2,37810
Water5,549308
1
A: Ras-related protein Rab-8A
B: Inositol polyphosphate 5-phosphatase OCRL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2095
Polymers36,5672
Non-polymers6433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-40 kcal/mol
Surface area14790 Å2
MethodPISA
2
C: Ras-related protein Rab-8A
D: Inositol polyphosphate 5-phosphatase OCRL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2095
Polymers36,5672
Non-polymers6433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-39 kcal/mol
Surface area15110 Å2
MethodPISA
3
E: Ras-related protein Rab-8A
F: Inositol polyphosphate 5-phosphatase OCRL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1134
Polymers36,5672
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-23 kcal/mol
Surface area16170 Å2
MethodPISA
4
G: Ras-related protein Rab-8A
H: Inositol polyphosphate 5-phosphatase OCRL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1134
Polymers36,5672
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-24 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.147, 55.340, 173.836
Angle α, β, γ (deg.)90.000, 91.930, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Ras-related protein Rab-8A / Oncogene c-mel


Mass: 20012.037 Da / Num. of mol.: 4 / Fragment: unp residues 6-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: synthetic DNASynthetic genomics / Gene: MEL, RAB8, RAB8A / Plasmid: pET19mod / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61006
#2: Protein
Inositol polyphosphate 5-phosphatase OCRL-1 / Lowe oculocerebrorenal syndrome protein


Mass: 16554.666 Da / Num. of mol.: 4 / Fragment: unp residues 540-678
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: synthetic DNASynthetic genomics / Gene: INPP5F, OCRL, OCRL1 / Plasmid: pOPINM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01968, phosphoinositide 5-phosphatase

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Non-polymers , 4 types, 318 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→47.378 Å / Num. obs: 99857 / % possible obs: 98.3 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 4.2 / % possible all: 97

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry codes 1r2q 2qv2

1r2q

2qv2


Resolution: 2→47.378 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.424 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 4996 5 %RANDOM
Rwork0.2079 ---
obs0.2096 99857 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 70.08 Å2 / Biso mean: 39.609 Å2 / Biso min: 15.68 Å2
Baniso -1Baniso -2Baniso -3
1--2.25 Å20 Å20.78 Å2
2--0.85 Å20 Å2
3---1.44 Å2
Refinement stepCycle: LAST / Resolution: 2→47.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9950 0 142 308 10400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210282
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.97913859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.91951209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08824.143519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.499151917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5491578
X-RAY DIFFRACTIONr_chiral_restr0.0990.21511
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027692
X-RAY DIFFRACTIONr_nbd_refined0.220.24418
X-RAY DIFFRACTIONr_nbtor_refined0.3140.27023
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2516
X-RAY DIFFRACTIONr_metal_ion_refined0.0180.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.2125
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.212
X-RAY DIFFRACTIONr_mcbond_it1.1471.56288
X-RAY DIFFRACTIONr_mcangle_it1.67529794
X-RAY DIFFRACTIONr_scbond_it2.70634632
X-RAY DIFFRACTIONr_scangle_it4.1644.54065
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 362 -
Rwork0.235 6893 -
all-7255 -
obs--96.85 %
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)
12.00530.0044-0.4850.7103-0.16111.58410.0682-0.05850.0548-0.04320.01-0.0555-0.1314-0.1134-0.0782-0.0142-0.00530.0074-0.01660.0089-0.07914.286315.13568.0846
21.74650.0547-0.2170.49220.07171.06950.065-0.10860.08880.0142-0.03580.0507-0.08220.1202-0.02910.0109-0.00680.0004-0.0328-0.0347-0.066171.1673-10.744618.7857
31.83740.60680.0321.4951-0.32710.89790.0205-0.0504-0.2489-0.0575-0.11630.00820.02330.11320.0959-0.0749-0.03940.0233-0.0119-0.0063-0.006356.008618.780763.946
41.362-0.4578-0.05980.86530.13141.00870.05610.0199-0.1704-0.011-0.1152-0.0490.0512-0.08360.059-0.0440.0179-0.0083-0.0679-0.00380.023519.4492-7.255622.199
52.33030.15260.49560.2924-0.02641.25570.0123-0.1979-0.38150.0035-0.0867-0.1461-0.0962-0.00720.0744-0.0639-0.0302-0.0107-0.06290.06280.058129.01492.966868.2764
61.1778-0.04940.22040.43910.12211.04290.0340.065-0.1045-0.035-0.10350.1424-0.0290.00890.0695-0.00340.0372-0.0153-0.0675-0.0411-0.006346.3293-22.880517.6377
72.5044-1.2415-0.6531.87460.11650.67920.12060.1149-0.281-0.1573-0.16090.5657-0.02350.13240.0403-0.0699-0.0309-0.0729-0.0537-0.06620.047140.621933.712851.8863
81.82320.6873-0.46270.68290.03890.41540.1009-0.07730.09940.0655-0.0607-0.03640.0197-0.0427-0.0401-0.0248-0.0002-0.0178-0.0693-0.0123-0.012334.99697.534134.2705
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 176
2X-RAY DIFFRACTION2C6 - 176
3X-RAY DIFFRACTION3E7 - 175
4X-RAY DIFFRACTION4G7 - 175
5X-RAY DIFFRACTION5B549 - 678
6X-RAY DIFFRACTION6D549 - 678
7X-RAY DIFFRACTION7F540 - 678
8X-RAY DIFFRACTION8H540 - 678

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