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- PDB-7a0v: Crystal structure of the 5-phosphatase domain of Synaptojanin1 in... -

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Basic information

Entry
Database: PDB / ID: 7a0v
TitleCrystal structure of the 5-phosphatase domain of Synaptojanin1 in complex with a nanobody
Components
  • Nanobody 13015
  • Synaptojanin-1
KeywordsHYDROLASE / Inositol polyphosphate 5-phosphatase / Phosphoinositide / Parkinson's disease / Epilepsy
Function / homology
Function and homology information


positive regulation of endosome organization / phosphatidylinositol phosphate 5-phosphatase activity / phosphatidylinositol-4-phosphate phosphatase activity / phosphatidylinositol phosphate 4-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / inositol-1,4,5-trisphosphate 5-phosphatase activity / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / synaptic vesicle uncoating ...positive regulation of endosome organization / phosphatidylinositol phosphate 5-phosphatase activity / phosphatidylinositol-4-phosphate phosphatase activity / phosphatidylinositol phosphate 4-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / inositol-1,4,5-trisphosphate 5-phosphatase activity / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / synaptic vesicle uncoating / inositol phosphate metabolic process / clathrin coat of coated pit / phosphoinositide 5-phosphatase / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol metabolic process / membrane coat / phosphatidylinositol dephosphorylation / phosphatidylinositol biosynthetic process / membrane organization / vesicle membrane / neurotransmitter transport / synaptic vesicle transport / synaptic vesicle priming / Synthesis of IP3 and IP4 in the cytosol / Synthesis of PIPs at the plasma membrane / synaptic vesicle endocytosis / synaptic membrane / learning / terminal bouton / presynapse / Clathrin-mediated endocytosis / perinuclear region of cytoplasm / RNA binding / membrane / cytoplasm / cytosol
Similarity search - Function
Synaptojanin-1, RNA recognition motif / Synaptojanin-1/2, RNA recognition motif / Domain of unknown function (DUF1866) / DUF1866 / SAC domain / SacI homology domain / Sac phosphatase domain profile. / : / Inositol polyphosphate-related phosphatase / Endonuclease/Exonuclease/phosphatase family 2 ...Synaptojanin-1, RNA recognition motif / Synaptojanin-1/2, RNA recognition motif / Domain of unknown function (DUF1866) / DUF1866 / SAC domain / SacI homology domain / Sac phosphatase domain profile. / : / Inositol polyphosphate-related phosphatase / Endonuclease/Exonuclease/phosphatase family 2 / Inositol polyphosphate phosphatase, catalytic domain homologues / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Synaptojanin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPaesmans, J. / Galicia, C. / Martin, E. / Versees, W.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0D3317N Belgium
Research Foundation - Flanders (FWO)1S04918N Belgium
Research Foundation - Flanders (FWO)1S09120N Belgium
CitationJournal: Elife / Year: 2020
Title: A structure of substrate-bound Synaptojanin1 provides new insights in its mechanism and the effect of disease mutations.
Authors: Paesmans, J. / Martin, E. / Deckers, B. / Berghmans, M. / Sethi, R. / Loeys, Y. / Pardon, E. / Steyaert, J. / Verstreken, P. / Galicia, C. / Versees, W.
History
DepositionAug 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptojanin-1
B: Nanobody 13015
C: Synaptojanin-1
D: Nanobody 13015
E: Synaptojanin-1
F: Nanobody 13015
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,00516
Polymers163,2796
Non-polymers72610
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The complex was purified via gel filtration.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10800 Å2
ΔGint-49 kcal/mol
Surface area52450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.874, 108.793, 100.974
Angle α, β, γ (deg.)90.000, 120.718, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-1141-

HOH

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Components

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Protein / Antibody , 2 types, 6 molecules ACEBDF

#1: Protein Synaptojanin-1 / Synaptic inositol 1 / 4 / 5-trisphosphate 5-phosphatase 1


Mass: 39866.387 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYNJ1, KIAA0910 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43426, phosphoinositide 5-phosphatase
#2: Antibody Nanobody 13015


Mass: 14559.901 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pMESy4 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 / Variant (production host): Su-

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Non-polymers , 4 types, 369 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 15% PEG 4000, 0.1 M sodium citrate pH 5, 10% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.980105 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980105 Å / Relative weight: 1
ReflectionResolution: 2.297→86.81 Å / Num. obs: 53823 / % possible obs: 92.3 % / Redundancy: 7 % / Biso Wilson estimate: 38.08 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.054 / Rrim(I) all: 0.143 / Net I/σ(I): 11.2
Reflection shellResolution: 2.3→2.43 Å / Num. unique obs: 1511 / CC1/2: 0.512

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSMar 15, 2019 (BUILT 20190806)data reduction
Aimless0.7.4data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1i9y, 3n9v, 3mtc, 4cmn, 4nc2

1i9y

3n9v

3mtc

4cmn

4nc2


Resolution: 2.3→86.81 Å / SU ML: 0.3193 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8898
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2523 2764 5.14 %
Rwork0.1964 51041 -
obs0.1992 53805 76.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.27 Å2
Refinement stepCycle: LAST / Resolution: 2.3→86.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10536 0 42 359 10937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001910851
X-RAY DIFFRACTIONf_angle_d0.4814688
X-RAY DIFFRACTIONf_chiral_restr0.3211583
X-RAY DIFFRACTIONf_plane_restr0.00331895
X-RAY DIFFRACTIONf_dihedral_angle_d21.97653886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.3588300.2746573X-RAY DIFFRACTION17.25
2.34-2.380.3252510.2834857X-RAY DIFFRACTION26.34
2.38-2.420.3671740.29281131X-RAY DIFFRACTION34.81
2.42-2.470.3144660.29261511X-RAY DIFFRACTION45.11
2.47-2.530.325990.28911947X-RAY DIFFRACTION58.57
2.53-2.590.35281310.27492329X-RAY DIFFRACTION70.59
2.59-2.630.35951000.2761803X-RAY DIFFRACTION79.26
2.7-2.720.3197620.2673986X-RAY DIFFRACTION89.19
2.72-2.80.36281730.26073279X-RAY DIFFRACTION98.97
2.8-2.890.32491910.24943282X-RAY DIFFRACTION100
2.89-30.2761760.24093317X-RAY DIFFRACTION100
3-3.120.27432100.22613277X-RAY DIFFRACTION100
3.12-3.260.28261820.22023330X-RAY DIFFRACTION99.97
3.26-3.430.25371980.20183286X-RAY DIFFRACTION100
3.43-3.650.24351800.17823325X-RAY DIFFRACTION100
3.65-3.930.21271660.17433333X-RAY DIFFRACTION99.97
3.93-4.320.20721820.1573333X-RAY DIFFRACTION100
4.32-4.950.18971630.14063360X-RAY DIFFRACTION99.97
4.95-6.230.21011840.17473351X-RAY DIFFRACTION100
6.23-86.810.25761460.19113431X-RAY DIFFRACTION99.44

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