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- PDB-5afp: Neuronal calcium sensor-1 (NCS-1)from Rattus norvegicus complex w... -

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Basic information

Entry
Database: PDB / ID: 5afp
TitleNeuronal calcium sensor-1 (NCS-1)from Rattus norvegicus complex with rhodopsin kinase peptide from Homo sapiens
Components
  • NEURONAL CALCIUM SENSOR 1
  • RHODOPSIN KINASE
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


calcium-dependent protein kinase inhibitor activity / rhodopsin kinase / rhodopsin kinase activity / calcium sensitive guanylate cyclase activator activity / G protein-coupled receptor kinase activity / regulation of opsin-mediated signaling pathway / regulation of presynaptic cytosolic calcium ion concentration / rhodopsin mediated signaling pathway / regulation of G protein-coupled receptor signaling pathway / presynaptic cytosol ...calcium-dependent protein kinase inhibitor activity / rhodopsin kinase / rhodopsin kinase activity / calcium sensitive guanylate cyclase activator activity / G protein-coupled receptor kinase activity / regulation of opsin-mediated signaling pathway / regulation of presynaptic cytosolic calcium ion concentration / rhodopsin mediated signaling pathway / regulation of G protein-coupled receptor signaling pathway / presynaptic cytosol / postsynaptic cytosol / regulation of synaptic vesicle exocytosis / regulation of neuron projection development / positive regulation of exocytosis / calyx of Held / voltage-gated calcium channel activity / positive regulation of calcium-mediated signaling / visual perception / photoreceptor disc membrane / Inactivation, recovery and regulation of the phototransduction cascade / postsynapse / postsynaptic density / protein autophosphorylation / protein kinase activity / axon / dendrite / glutamatergic synapse / calcium ion binding / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / magnesium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Rhodopsin kinase GRK1 / Rhodopsin kinase, catalytic domain / GPCR kinase / Recoverin family / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / EF hand ...Rhodopsin kinase GRK1 / Rhodopsin kinase, catalytic domain / GPCR kinase / Recoverin family / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / EF hand / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Neuronal calcium sensor 1 / Rhodopsin kinase GRK1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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.Y.
History
DepositionJan 23, 2015Deposition site: PDBE / Processing site: PDBE
SupersessionMar 18, 2015ID: 4UYC
Revision 1.0Mar 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
C: RHODOPSIN KINASE
D: RHODOPSIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,19312
Polymers48,9074
Non-polymers2868
Water46826
1
B: NEURONAL CALCIUM SENSOR 1
C: RHODOPSIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5745
Polymers24,4532
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-63.2 kcal/mol
Surface area9900 Å2
MethodPISA
2
A: NEURONAL CALCIUM SENSOR 1
D: RHODOPSIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6207
Polymers24,4532
Non-polymers1665
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-63.3 kcal/mol
Surface area10030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.690, 93.690, 55.710
Angle α, β, γ (deg.)90.00, 92.25, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (-1), (-1) / Vector: 19.1, -22.5, 28.7)

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Components

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


Mass: 21902.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Cell: NEURON / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62168
#2: Protein/peptide RHODOPSIN KINASE / / RK / G PROTEIN-COUPLED RECEPTOR KINASE 1


Mass: 2550.777 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-25 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q15835
#3: Chemical
ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 7.5
Details: 0.12M ALCOHOLS (1,6-HEXANEDIOL; 1- BUTANOL;1,PROPANEDIOL(RACEMIC); 2-PROPONOL; 1, 4-BUTANEDIOL; 1,3- PROPANEDIOL); 0.1M BUFFER 2 (SODIUM HEPES; MOPS ACID PH 7.5); P550MME_P20K 30%.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9
DetectorDate: Jul 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→48 Å / Num. obs: 18488 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.8
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.2 / % possible all: 94.3

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Processing

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

2you
PDB Unreleased entry


Resolution: 2.3→47.86 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / SU B: 17.091 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.395 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25515 956 5.2 %RANDOM
Rwork0.22556 ---
obs0.22708 17512 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.458 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å2-0.34 Å2
2---0.36 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2988 0 8 26 3022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.023092
X-RAY DIFFRACTIONr_bond_other_d00.022866
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9554105
X-RAY DIFFRACTIONr_angle_other_deg0.73836615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9135362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0225.25160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32815544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5741514
X-RAY DIFFRACTIONr_chiral_restr0.0760.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023437
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02705
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_it1.6893.0271476
X-RAY DIFFRACTIONr_mcbond_other1.6823.0271475
X-RAY DIFFRACTIONr_mcangle_it2.4524.5171822
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3873.3141616
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 66 -
Rwork0.284 1229 -
obs--93.98 %
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)
10.7874-0.344-0.89010.8509-0.09673.18330.0360.01180.00210.00520.0271-0.06880.0522-0.003-0.06310.0089-0.0043-0.00570.1293-0.01220.10417.06760.828424.7305
20.89440.91431.0752.00670.17073.246-0.03380.04140.029-0.07720.0465-0.0445-0.16480.0597-0.01270.03480.00510.04780.1323-0.02320.1342-2.4361-23.29113.9847
37.07280.51285.88264.65741.30166.87630.11220.1951-0.19170.19990.1391-0.13280.20450.2939-0.25140.1203-0.00320.02670.2149-0.03730.14280.4399-28.6291.936
44.4075-0.7208-5.67745.6113-0.36437.68960.2337-0.02240.15630.10420.0282-0.2423-0.2884-0.017-0.26190.1754-0.0106-0.02080.2583-0.01130.223919.79026.146326.9352
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 185
2X-RAY DIFFRACTION2B6 - 184
3X-RAY DIFFRACTION3C6 - 17
4X-RAY DIFFRACTION4D5 - 17

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