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- PDB-5g08: Crystal structure of Drosophila NCS-1 bound to chlorpromazine -

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Basic information

Entry
Database: PDB / ID: 5g08
TitleCrystal structure of Drosophila NCS-1 bound to chlorpromazine
ComponentsFREQUENIN 2Neuronal calcium sensor-1
KeywordsSIGNALING PROTEIN / CALCIUM SENSOR
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-Z80 / Frequenin-2
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsChaves-Sanjuan, A. / Infantes, L. / Sanchez-Barrena, M.J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Interference of the complex between NCS-1 and Ric8a with phenothiazines regulates synaptic function and is an approach for fragile X syndrome.
Authors: Mansilla, A. / Chaves-Sanjuan, A. / Campillo, N.E. / Semelidou, O. / Martinez-Gonzalez, L. / Infantes, L. / Gonzalez-Rubio, J.M. / Gil, C. / Conde, S. / Skoulakis, E.M. / Ferrus, A. / ...Authors: Mansilla, A. / Chaves-Sanjuan, A. / Campillo, N.E. / Semelidou, O. / Martinez-Gonzalez, L. / Infantes, L. / Gonzalez-Rubio, J.M. / Gil, C. / Conde, S. / Skoulakis, E.M. / Ferrus, A. / Martinez, A. / Sanchez-Barrena, M.J.
History
DepositionMar 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Dec 27, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Dec 7, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: FREQUENIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6088
Polymers21,9221
Non-polymers6857
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.217, 54.917, 60.210
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 FREQUENIN 2 / Neuronal calcium sensor-1


Mass: 21922.443 Da / Num. of mol.: 1 / Mutation: YES [I178M]
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PETDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9VWX8

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Non-polymers , 5 types, 174 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-Z80 / 3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine / Chlorpromazine / Chlorpromazine


Mass: 318.864 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19ClN2S / Comment: medication, antipsychotic*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence details178M

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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: 2.05 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growDetails: 20% W/V PEG MME 2K, 0.1M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97872
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.52→40.57 Å / Num. obs: 28243 / % possible obs: 100 % / Observed criterion σ(I): 0.8 / Redundancy: 12.4 % / Biso Wilson estimate: 28.18 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.5
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BY4

4by4


Resolution: 1.52→40.575 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 30.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 1420 5 %
Rwork0.1926 --
obs0.1939 28243 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.1 Å2
Refinement stepCycle: LAST / Resolution: 1.52→40.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1497 0 40 167 1704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111611
X-RAY DIFFRACTIONf_angle_d1.0882167
X-RAY DIFFRACTIONf_dihedral_angle_d24.495987
X-RAY DIFFRACTIONf_chiral_restr0.059216
X-RAY DIFFRACTIONf_plane_restr0.007284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.57430.37681390.38512617X-RAY DIFFRACTION99
1.5743-1.63740.29751100.29992680X-RAY DIFFRACTION100
1.6374-1.71190.30491340.26092636X-RAY DIFFRACTION100
1.7119-1.80210.29531460.24552658X-RAY DIFFRACTION100
1.8021-1.91510.24811300.24192649X-RAY DIFFRACTION100
1.9151-2.06290.26331430.22342658X-RAY DIFFRACTION100
2.0629-2.27050.22571320.19542699X-RAY DIFFRACTION99
2.2705-2.5990.23271600.19272672X-RAY DIFFRACTION100
2.599-3.27420.21821590.18812708X-RAY DIFFRACTION100
3.2742-40.58910.18571670.16692847X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9761-0.1282-0.66281.9058-0.99111.86070.00940.2258-0.2560.0374-0.01420.36720.4263-0.26050.00010.3401-0.01550.01170.3087-0.01360.329918.9168-30.7754-9.3508
22.27420.0924-0.2210.55380.96251.7415-0.00880.352-0.30260.07430.07070.09690.2264-0.29590.00150.2422-0.0275-0.01640.29810.03510.294.1055-16.2915-13.3405
31.7273-0.28730.6351.4484-0.4080.37180.00870.2792-0.1339-0.09880.0085-0.08130.07750.1008-0.00050.2432-0.00110.01940.2562-0.00590.22218.6013-15.7724-9.7754
41.41170.70020.70510.9413-0.14210.9013-0.05770.0850.56430.12260.22180.2298-0.3066-0.18570.00020.26880.03460.01340.27390.06690.303810.41-0.3905-12.1346
50.7236-0.3677-0.1320.2321-0.11841.1433-0.233-0.45811.04090.37750.13440.5446-0.4136-0.8215-0.00310.59460.12780.08680.5776-0.0420.68245.2557.814-3.6234
61.33530.0823-0.5250.94890.76630.88160.2173-0.29060.54720.6697-0.1896-0.4155-0.71750.1685-0.00090.3398-0.01930.02130.25420.0010.294722.91414.0323-6.2012
70.0061-0.00830.02010.0527-0.15560.47420.7754-1.34250.59830.5249-0.45350.44670.3648-0.66960.00550.5997-0.06120.0450.68580.02210.433312.3204-3.11020.1287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 4 THROUGH 37 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 38 THROUGH 72 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 73 THROUGH 108 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 109 THROUGH 132 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 133 THROUGH 155 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 156 THROUGH 174 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 175 THROUGH 187 )

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