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- PDB-6epa: Structure of dNCS-1 bound to the NCS-1/Ric8a protein/protein inte... -

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Basic information

Entry
Database: PDB / ID: 6epa
TitleStructure of dNCS-1 bound to the NCS-1/Ric8a protein/protein interaction regulator IGS-1.76
ComponentsFI18190p1
KeywordsSIGNALING PROTEIN / Calcium sensor / synapse regulation
Function / homology
Function and homology information


calcium sensitive guanylate cyclase activator activity / regulation of neurotransmitter secretion / neurotransmitter secretion / neuromuscular junction development / vesicle-mediated transport / synaptic vesicle / chemical synaptic transmission / calcium ion binding / cytoplasm
Similarity search - Function
Recoverin family / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain ...Recoverin family / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-BNQ / Frequenin-2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsSanchez-Barrena, M.J. / Daniel, M. / Infantes, L.
Funding support Spain, 4items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2011-28184-C02-02 Spain
Spanish Ministry of Economy and CompetitivenessBFU2014-59796-R Spain
Spanish Ministry of Economy and CompetitivenessRYC-2008-03449 Spain
European Commission - InstructR&D Pilot Project APPID 99 Spain
CitationJournal: J. Med. Chem. / Year: 2018
Title: Deciphering the Inhibition of the Neuronal Calcium Sensor 1 and the Guanine Exchange Factor Ric8a with a Small Phenothiazine Molecule for the Rational Generation of Therapeutic Synapse Function Regulators.
Authors: Roca, C. / Martinez-Gonzalez, L. / Daniel-Mozo, M. / Sastre, J. / Infantes, L. / Mansilla, A. / Chaves-Sanjuan, A. / Gonzalez-Rubio, J.M. / Gil, C. / Canada, F.J. / Martinez, A. / Sanchez- ...Authors: Roca, C. / Martinez-Gonzalez, L. / Daniel-Mozo, M. / Sastre, J. / Infantes, L. / Mansilla, A. / Chaves-Sanjuan, A. / Gonzalez-Rubio, J.M. / Gil, C. / Canada, F.J. / Martinez, A. / Sanchez-Barrena, M.J. / Campillo, N.E.
History
DepositionOct 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FI18190p1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5447
Polymers21,9221
Non-polymers6226
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Trp Emission Fluorescence
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-43 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.843, 55.456, 61.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FI18190p1 / Frequenin 2 / isoform A / isoform B / isoform C / isoform D


Mass: 21922.443 Da / Num. of mol.: 1
Mutation: As reported in a previous publication (Romero-Pozuelo et al., JCS 2014) Drosophila Frq2 suffers edition process and besides de curated sequence, the I178M mutant also exists naturally
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Frq2, Dmel\CG5907, Frq, frq, frq2, Frq2-RA, CG5907, Dmel_CG5907
Production host: Escherichia coli (E. coli) / References: UniProt: Q9VWX8

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Non-polymers , 5 types, 171 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BNQ / ~{N}-(1,3-benzothiazol-2-yl)-3,3-diphenyl-propanamide


Mass: 358.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18N2OS
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes pH 7.5 and 25% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979256 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979256 Å / Relative weight: 1
ReflectionResolution: 1.82→41.112 Å / Num. obs: 116619 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rpim(I) all: 0.029 / Net I/σ(I): 14.4
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1008 / CC1/2: 0.389 / Rpim(I) all: 0.825 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4by4

4by4


Resolution: 1.82→41.112 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 25.93
RfactorNum. reflection% reflection
Rfree0.2319 1573 4.87 %
Rwork0.1886 --
obs0.1905 32275 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.82→41.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 36 165 1719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081645
X-RAY DIFFRACTIONf_angle_d0.5542192
X-RAY DIFFRACTIONf_dihedral_angle_d16.696985
X-RAY DIFFRACTIONf_chiral_restr0.037222
X-RAY DIFFRACTIONf_plane_restr0.003292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8201-1.87880.3291090.33932774X-RAY DIFFRACTION98
1.8788-1.9460.37711440.31012813X-RAY DIFFRACTION100
1.946-2.02390.30761500.28012773X-RAY DIFFRACTION100
2.0239-2.1160.30521730.24332789X-RAY DIFFRACTION100
2.116-2.22760.29271100.21942815X-RAY DIFFRACTION100
2.2276-2.36710.26671590.20342795X-RAY DIFFRACTION100
2.3671-2.54980.23271750.18542745X-RAY DIFFRACTION100
2.5498-2.80640.1871620.17062772X-RAY DIFFRACTION100
2.8064-3.21230.2521620.17562795X-RAY DIFFRACTION100
3.2123-4.04670.1991200.16222803X-RAY DIFFRACTION100
4.0467-41.12270.19251090.16812828X-RAY DIFFRACTION100

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