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- PDB-5aeq: Neuronal calcium sensor (NCS-1)from Rattus norvegicus -

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Basic information

Entry
Database: PDB / ID: 5aeq
TitleNeuronal calcium sensor (NCS-1)from Rattus norvegicus
ComponentsNEURONAL CALCIUM SENSOR 1
KeywordsSIGNALING PROTEIN / CALCIUM SENSOR
Function / homology
Function and homology information


calcium-dependent protein kinase inhibitor activity / calcium sensitive guanylate cyclase activator activity / regulation of presynaptic cytosolic calcium ion concentration / dense core granule / regulation of neuron projection development / regulation of synaptic vesicle exocytosis / positive regulation of exocytosis / regulation of signal transduction / postsynaptic cytosol / voltage-gated calcium channel activity ...calcium-dependent protein kinase inhibitor activity / calcium sensitive guanylate cyclase activator activity / regulation of presynaptic cytosolic calcium ion concentration / dense core granule / regulation of neuron projection development / regulation of synaptic vesicle exocytosis / positive regulation of exocytosis / regulation of signal transduction / postsynaptic cytosol / voltage-gated calcium channel activity / presynaptic cytosol / positive regulation of calcium-mediated signaling / calyx of Held / postsynapse / postsynaptic density / axon / calcium ion binding / dendrite / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / magnesium ion binding / Golgi apparatus / plasma membrane / cytoplasm
Similarity search - Function
Recoverin family / EF hand domain / 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 domain / 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
Neuronal calcium sensor 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSaleem, M. / Karuppiah, V. / Pandalaneni, S. / Burgoyne, R. / Derrick, J.P. / Lian, L.Y.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Neuronal Calcium Sensor-1 Binds the D2 Dopamine Receptor and G-Protein-Coupled Receptor Kinase 1 (Grk1) Peptides Using Different Modes of Interactions.
Authors: Pandalaneni, S. / Karuppiah, V. / Saleem, M. / Haynes, L.P. / Burgoyne, R.D. / Mayans, O. / Derrick, J.P. / Lian, L.
History
DepositionJan 8, 2015Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 18, 2015ID: 2YOV
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Aug 5, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEURONAL CALCIUM SENSOR 1
B: NEURONAL CALCIUM SENSOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,09210
Polymers43,8052
Non-polymers2868
Water2,540141
1
A: NEURONAL CALCIUM SENSOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0465
Polymers21,9031
Non-polymers1434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NEURONAL CALCIUM SENSOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0465
Polymers21,9031
Non-polymers1434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.910, 55.490, 77.360
Angle α, β, γ (deg.)90.00, 94.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.159, -0.001, -0.987), (0.011, 0.999, -0.003), (0.987, -0.0124, -0.159)
Vector: 76.46, 10.17, 30)

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Components

#1: Protein NEURONAL CALCIUM SENSOR 1 / NCS-1 / FREQUENIN HOMOLOG / FREQUENIN-LIKE PROTEIN / FREQUENIN-LIKE UBIQUITOUS PROTEIN / NEURONAL ...NCS-1 / FREQUENIN HOMOLOG / FREQUENIN-LIKE PROTEIN / FREQUENIN-LIKE UBIQUITOUS PROTEIN / NEURONAL CALCIUM SENSOR


Mass: 21902.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Tissue: NEURON / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P62168
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.95→54 Å / Num. obs: 32357 / % possible obs: 96.9 % / Observed criterion σ(I): 3 / Redundancy: 2.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.7
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.6 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YOU

2you
PDB Unreleased entry


Resolution: 1.95→77.13 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.895 / SU B: 8.103 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 1631 5 %RANDOM
Rwork0.22499 ---
obs0.22647 30711 96.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.736 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å2-1.01 Å2
2---0.88 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.95→77.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 8 141 2941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022894
X-RAY DIFFRACTIONr_bond_other_d00.022660
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.9573827
X-RAY DIFFRACTIONr_angle_other_deg0.71136150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7725338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33525.329152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54615518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1081514
X-RAY DIFFRACTIONr_chiral_restr0.0710.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023215
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02655
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_it1.1161.491377
X-RAY DIFFRACTIONr_mcbond_other1.1071.4871374
X-RAY DIFFRACTIONr_mcangle_it1.722.2171700
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7641.7271517
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 105 -
Rwork0.262 2327 -
obs--97.67 %
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)
10.3646-0.62130.00692.31770.58570.29110.02660.0490.0722-0.0759-0.0037-0.1801-0.01920.0218-0.02280.02610.00270.01910.04590.00320.024210.5934-1.839436.4543
20.18890.0143-0.18711.4569-0.34770.51280.05360.0265-0.0287-0.0247-0.04020.12590.14560.0285-0.01340.20160.0086-0.05020.05650.00760.040616.3374-10.421264.1113
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 189
2X-RAY DIFFRACTION2B10 - 185

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