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- PDB-4lt7: Crystal structure of the c2a domain of rabphilin-3a in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4lt7
TitleCrystal structure of the c2a domain of rabphilin-3a in complex with a calcium
ComponentsRabphilin-3A
KeywordsPROTEIN TRANSPORT / calcium binding / C2 domain / signal transduction
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
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVerdaguer, N. / Ferrer-Orta, C. / Buxaderas, M. / Corbalan-Garcia, S. / Perez-Sanchez, D. / Guerrero-Valero, M. / Luengo, G. / Pous, J. / Guerra, P. / Gomez-Fernandez, J.C. / Guillen, J.
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
DepositionJul 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name
Revision 1.3Sep 20, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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)15,3462
Polymers15,3051
Non-polymers401
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.690, 40.030, 90.250
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 1 domain 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 10 mM CaCl2, 150mM NaCl, 25mM HEPES ph 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5417 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 10, 2012 / Details: mirrors
RadiationMonochromator: osmic confocals focusing optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 3660 / % possible obs: 72.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 3.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 1.9 / % possible all: 68.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CHD

2chd


Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.891 / SU B: 31.97 / SU ML: 0.305 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.447 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28943 164 4.5 %RANDOM
Rwork0.24318 ---
obs0.24531 3490 70.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.055 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å2-0 Å2
2--0.37 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1019 0 1 1 1021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191035
X-RAY DIFFRACTIONr_bond_other_d0.0010.021012
X-RAY DIFFRACTIONr_angle_refined_deg0.9341.9671393
X-RAY DIFFRACTIONr_angle_other_deg0.64332320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8125127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59723.87849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53815196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.574159
X-RAY DIFFRACTIONr_chiral_restr0.0550.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021167
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02244
X-RAY DIFFRACTIONr_mcbond_it0.4332.005511
X-RAY DIFFRACTIONr_mcbond_other0.4332.004510
X-RAY DIFFRACTIONr_mcangle_it0.7983.007637
X-RAY DIFFRACTIONr_mcangle_other0.7983.007638
X-RAY DIFFRACTIONr_scbond_it0.3422.034524
X-RAY DIFFRACTIONr_scbond_other0.3412.034525
X-RAY DIFFRACTIONr_scangle_other0.633.02757
X-RAY DIFFRACTIONr_long_range_B_refined2.19915.0431054
X-RAY DIFFRACTIONr_long_range_B_other2.19815.0491055
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 10 -
Rwork0.295 233 -
obs--65.15 %
Refinement TLS params.Method: refined / Origin x: 10.4876 Å / Origin y: 9.8121 Å / Origin z: 32.0332 Å
111213212223313233
T0.2666 Å2-0.0125 Å2-0.0244 Å2-0.134 Å20.0179 Å2--0.1107 Å2
L3.8746 °2-0.8191 °2-2.975 °2-2.133 °21.969 °2--6.3323 °2
S0.1271 Å °0.1722 Å °-0.1103 Å °-0.1218 Å °-0.2594 Å °0.1194 Å °0.0616 Å °-0.3676 Å °0.1323 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A382 - 509
2X-RAY DIFFRACTION1A701

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