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- PDB-4np9: Structure of Rabphilin C2A domain bound to IP3 -

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Basic information

Entry
Database: PDB / ID: 4np9
TitleStructure of Rabphilin C2A domain bound to IP3
ComponentsRabphilin-3A
KeywordsPROTEIN TRANSPORT / RABPHILIN-3A / C2 DOMAIN / C2A / CALCIUM BINDING / SYNAPTIC EXOCYTOSIS METAL-BINDING / C-2 domain fold / EXOPHILIN-1
Function / homology
Function and homology information


selenium binding / spontaneous neurotransmitter secretion / extrinsic component of synaptic vesicle membrane / regulation of calcium ion-dependent exocytosis / cholinergic synapse / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / dendritic spine organization / synaptic vesicle priming / extrinsic component of membrane ...selenium binding / spontaneous neurotransmitter secretion / extrinsic component of synaptic vesicle membrane / regulation of calcium ion-dependent exocytosis / cholinergic synapse / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / dendritic spine organization / synaptic vesicle priming / extrinsic component of membrane / phosphate ion binding / exocytosis / regulation of NMDA receptor activity / phosphatidylinositol-4,5-bisphosphate binding / secretory granule / phospholipid binding / intracellular protein transport / neuromuscular junction / synaptic vesicle membrane / small GTPase binding / synaptic vesicle / postsynaptic membrane / dendritic spine / neuron projection / synapse / calcium ion binding / protein-containing complex binding / protein-containing complex / zinc ion binding
Similarity search - Function
Rabphilin-3A / : / Rabphilin/DOC2/Noc2 / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Synaptotagmin ...Rabphilin-3A / : / Rabphilin/DOC2/Noc2 / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Synaptotagmin / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / 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
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Rabphilin-3A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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 21, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rabphilin-3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8223
Polymers15,3051
Non-polymers5162
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.27, 39.47, 89.26
Angle α, β, γ (deg.)90, 90, 90
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 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P47709
#2: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol trisphosphate


Mass: 420.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O15P3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 25-28% PEG 4K, 10-20mM Ammonium sulfate, 100mM HEPES pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2012
RadiationMonochromator: Monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.92→44.93 Å / Num. all: 11230 / Num. obs: 10862 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.087 / Rsym value: 0.088 / Net I/σ(I): 13.19
Reflection shellResolution: 1.92→2.041 Å / Redundancy: 50.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1687 / Rsym value: 0.35 / % possible all: 95

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Processing

Software
NameVersionClassification
DNAdata collection
REFMACrefinement
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→29.566 Å / SU ML: 0.26 / σ(F): 0.02 / Phase error: 25.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 520 4.84 %RANDOM
Rwork0.2089 ---
all0.2501 10862 --
obs0.2108 10754 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→29.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 0 29 139 1204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041080
X-RAY DIFFRACTIONf_angle_d0.9031459
X-RAY DIFFRACTIONf_dihedral_angle_d15.171418
X-RAY DIFFRACTIONf_chiral_restr0.034163
X-RAY DIFFRACTIONf_plane_restr0.003184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.92-2.11320.29281240.2209249998
2.1132-2.41880.26381380.2178246398
2.4188-3.0470.25221360.20192576100
3.047-29.56980.23231220.20682696100

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