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- PDB-4ns0: The C2A domain of Rabphilin 3A in complex with PI(4,5)P2 -

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Basic information

Entry
Database: PDB / ID: 4ns0
TitleThe C2A domain of Rabphilin 3A in complex with PI(4,5)P2
ComponentsRabphilin-3A
KeywordsPROTEIN TRANSPORT / C2 domain / Calcium binding / phospholipid binding / RABPHILIN-3A / C2A / SYNAPTIC EXOCYTOSIS METAL-BINDING / C-2 domain fold / EXOPHILIN-1
Function / homology
Function and homology information


selenium binding / spontaneous neurotransmitter secretion / calcium-dependent activation of synaptic vesicle fusion / positive regulation of calcium ion-dependent exocytosis / cholinergic synapse / extrinsic component of synaptic vesicle membrane / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / dendritic spine organization / regulation of NMDA receptor activity ...selenium binding / spontaneous neurotransmitter secretion / calcium-dependent activation of synaptic vesicle fusion / positive regulation of calcium ion-dependent exocytosis / cholinergic synapse / extrinsic component of synaptic vesicle membrane / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / dendritic spine organization / regulation of NMDA receptor activity / extrinsic component of membrane / synaptic vesicle priming / phosphate ion binding / phosphatidylinositol-4,5-bisphosphate binding / secretory granule / intracellular protein transport / neuromuscular junction / phospholipid binding / small GTPase binding / synaptic vesicle membrane / synaptic vesicle / dendritic spine / postsynaptic membrane / neuron projection / synapse / calcium ion binding / protein-containing complex binding / protein-containing complex / zinc ion binding
Similarity search - Function
Rabphilin-3A / Rabphilin/DOC2/Noc2 / : / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Synaptotagmin ...Rabphilin-3A / Rabphilin/DOC2/Noc2 / : / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-PIO / Rabphilin-3A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGuillen, J. / Ferrer-Orta, C. / Buxaderas, M. / Perez-sanchez, D. / Guerrero-Valero, M. / Luengo-Gil, G. / Pous, J. / Guerra, P. / Gomez-Fernandez, J.C. / Verdaguer, N. / Corbalan-Garcia, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural insights into the Ca2+ and PI(4,5)P2 binding modes of the C2 domains of rabphilin 3A and synaptotagmin 1.
Authors: Guillen, J. / Ferrer-Orta, C. / Buxaderas, M. / Perez-Sanchez, D. / Guerrero-Valero, M. / Luengo-Gil, G. / Pous, J. / Guerra, P. / Gomez-Fernandez, J.C. / Verdaguer, N. / Corbalan-Garcia, S.
History
DepositionNov 27, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations / Category: citation / database_2 / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rabphilin-3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1483
Polymers15,3051
Non-polymers8432
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.970, 38.910, 88.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Rabphilin-3A / Exophilin-1


Mass: 15305.478 Da / Num. of mol.: 1 / Fragment: C2 domain, UNP RESIDUES 378-510
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rph3a / Production host: Escherichia coli (E. coli) / References: UniProt: P47709
#2: Chemical ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H49O19P3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25mM Hepes, 20mM Ammonuim Sulphate, 25% PEG 4K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.93
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.8→44.36 Å / Num. obs: 12421 / % possible obs: 94.2 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.131 / Rsym value: 0.061 / Net I/σ(I): 15
Reflection shellResolution: 1.78→1.89 Å / Rmerge(I) obs: 0.72 / % possible all: 96.9

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Processing

Software
NameVersionClassification
DNAdata collection
XFITdata reduction
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CHD

2chd


Resolution: 1.8→44.36 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.744 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22604 635 5 %RANDOM
Rwork0.18405 ---
obs0.18612 12047 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.048 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å20 Å2
2---0.1 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1019 0 39 113 1171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191077
X-RAY DIFFRACTIONr_bond_other_d0.0010.021029
X-RAY DIFFRACTIONr_angle_refined_deg1.22.0071457
X-RAY DIFFRACTIONr_angle_other_deg0.98232366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6115129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.00623.87849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6315197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.48159
X-RAY DIFFRACTIONr_chiral_restr0.1830.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021178
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02245
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0862.221513
X-RAY DIFFRACTIONr_mcbond_other1.072.219512
X-RAY DIFFRACTIONr_mcangle_it1.8673.323640
X-RAY DIFFRACTIONr_mcangle_other1.9293.297640
X-RAY DIFFRACTIONr_scbond_it1.2652.497564
X-RAY DIFFRACTIONr_scbond_other1.2532.472566
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0663.639820
X-RAY DIFFRACTIONr_long_range_B_refined6.69418.8651224
X-RAY DIFFRACTIONr_long_range_B_other5.92818.2321184
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 46 -
Rwork0.375 873 -
obs--99.78 %

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