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

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Basic information

Entry
Database: PDB / ID: 5aer
TitleNeuronal calcium sensor-1 (NCS-1)from Rattus norvegicus complex with D2 dopamine receptor peptide from Homo sapiens
Components
  • D(2) DOPAMINE RECEPTOR
  • NEURONAL CALCIUM SENSOR 1
KeywordsSIGNALING PROTEIN / NEURONAL CALCIUM SENSOR-1 / DOPAMINE RECEPTOR 2
Function / homology
Function and homology information


calcium-dependent protein kinase inhibitor activity / negative regulation of dopamine receptor signaling pathway / positive regulation of dopamine uptake involved in synaptic transmission / negative regulation of dephosphorylation / negative regulation of circadian sleep/wake cycle, sleep / positive regulation of glial cell-derived neurotrophic factor production / acid secretion / calcium sensitive guanylate cyclase activator activity / dopamine neurotransmitter receptor activity, coupled via Gi/Go / nervous system process involved in regulation of systemic arterial blood pressure ...calcium-dependent protein kinase inhibitor activity / negative regulation of dopamine receptor signaling pathway / positive regulation of dopamine uptake involved in synaptic transmission / negative regulation of dephosphorylation / negative regulation of circadian sleep/wake cycle, sleep / positive regulation of glial cell-derived neurotrophic factor production / acid secretion / calcium sensitive guanylate cyclase activator activity / dopamine neurotransmitter receptor activity, coupled via Gi/Go / nervous system process involved in regulation of systemic arterial blood pressure / response to histamine / regulation of synapse structural plasticity / regulation of locomotion involved in locomotory behavior / neuron-neuron synaptic transmission / adenohypophysis development / negative regulation of dopamine secretion / positive regulation of renal sodium excretion / negative regulation of cellular response to hypoxia / regulation of potassium ion transport / hyaloid vascular plexus regression / adenylate cyclase-inhibiting dopamine receptor signaling pathway / response to inactivity / orbitofrontal cortex development / cerebral cortex GABAergic interneuron migration / Dopamine receptors / negative regulation of neuron migration / dopamine binding / branching morphogenesis of a nerve / regulation of dopamine uptake involved in synaptic transmission / positive regulation of growth hormone secretion / phospholipase C-activating dopamine receptor signaling pathway / peristalsis / heterotrimeric G-protein binding / drinking behavior / G protein-coupled receptor complex / grooming behavior / behavioral response to ethanol / regulation of presynaptic cytosolic calcium ion concentration / auditory behavior / positive regulation of G protein-coupled receptor signaling pathway / striatum development / dopaminergic synapse / dense core granule / positive regulation of urine volume / positive regulation of multicellular organism growth / G protein-coupled receptor internalization / negative regulation of synaptic transmission, glutamatergic / non-motile cilium / heterocyclic compound binding / response to iron ion / adult walking behavior / arachidonate secretion / response to morphine / ciliary membrane / negative regulation of cytosolic calcium ion concentration / regulation of synaptic transmission, GABAergic / temperature homeostasis / pigmentation / positive regulation of neuroblast proliferation / positive regulation of cytokinesis / dopamine uptake involved in synaptic transmission / regulation of neuron projection development / regulation of dopamine secretion / regulation of synaptic vesicle exocytosis / dopamine metabolic process / cellular response to ethanol / response to light stimulus / positive regulation of exocytosis / associative learning / positive regulation of receptor internalization / lateral plasma membrane / endocytic vesicle / G-protein alpha-subunit binding / neuroblast proliferation / negative regulation of protein secretion / regulation of signal transduction / postsynaptic cytosol / long-term memory / potassium channel regulator activity / sperm flagellum / prepulse inhibition / response to axon injury / postsynaptic modulation of chemical synaptic transmission / voltage-gated calcium channel activity / behavioral response to cocaine / presynaptic cytosol / regulation of sodium ion transport / negative regulation of blood pressure / synapse assembly / cellular response to retinoic acid / axon terminus / release of sequestered calcium ion into cytosol / ionotropic glutamate receptor binding / presynaptic modulation of chemical synaptic transmission / acrosomal vesicle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / axonogenesis / positive regulation of calcium-mediated signaling / regulation of heart rate / calyx of Held
Similarity search - Function
Dopamine D2 receptor / Dopamine receptor family / Recoverin family / EF hand domain / EF-hand / Recoverin; domain 1 / Serpentine type 7TM GPCR chemoreceptor Srsx / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...Dopamine D2 receptor / Dopamine receptor family / Recoverin family / EF hand domain / EF-hand / Recoverin; domain 1 / Serpentine type 7TM GPCR chemoreceptor Srsx / 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 / G-protein coupled receptors family 1 signature. / EF-hand domain pair / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / D(2) dopamine receptor / Neuronal calcium sensor 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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: 2YOU
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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: D(2) DOPAMINE RECEPTOR
C: D(2) DOPAMINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5027
Polymers25,3433
Non-polymers1594
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-24.1 kcal/mol
Surface area10110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.670, 44.670, 205.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.58, -0.75, 0.3), (-0.8, 0.6, -0.047), (-0.15, -0.27, -0.95)
Vector: 19.3, 3.2, -32.7)

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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-1


Mass: 21902.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Tissue: NEURON / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62168
#2: Protein/peptide D(2) DOPAMINE RECEPTOR / DOPAMINE D2 RECEPTOR


Mass: 1720.066 Da / Num. of mol.: 2 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P14416
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917
DetectorType: MARRESEARCH MARMOSAIC 300MM / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.19→51 Å / Num. obs: 11235 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15
Reflection shellResolution: 2.19→2.25 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.4 / % possible all: 77.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G8I

1g8i


Resolution: 2.19→51.38 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.933 / SU B: 14.902 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25577 1106 10 %RANDOM
Rwork0.21661 ---
obs0.22051 9975 95.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.19→51.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 4 30 1754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021776
X-RAY DIFFRACTIONr_bond_other_d0.0010.021665
X-RAY DIFFRACTIONr_angle_refined_deg0.9071.9582363
X-RAY DIFFRACTIONr_angle_other_deg0.633837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8715206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.78224.83993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60315319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.823159
X-RAY DIFFRACTIONr_chiral_restr0.0560.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02417
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_it1.3082.773836
X-RAY DIFFRACTIONr_mcbond_other1.3072.772835
X-RAY DIFFRACTIONr_mcangle_it1.8434.1481036
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9422.993937
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: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 61 -
Rwork0.269 559 -
obs--74.07 %
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)
10.8028-0.1014-0.09511.75020.0452.71230.10460.0459-0.16820.0710.0062-0.09380.11020.1456-0.11070.02540.0203-0.02380.02960.00610.0795-11.668220.9158-19.5944
25.5765-1.796-2.83452.8571-2.93397.93490.21790.17080.1837-0.0464-0.272-0.1489-0.15420.26820.05410.0629-0.0440.01520.1055-0.00670.0924-6.246529.9611-27.9642
32.596-0.3801-1.68995.8398-2.89852.8124-0.07930.01550.14440.13660.1123-0.1043-0.0128-0.0531-0.0330.1077-0.0852-0.02120.1401-0.01210.0972-6.945634.8385-14.7331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 190
2X-RAY DIFFRACTION2B430 - 443
3X-RAY DIFFRACTION3C430 - 443

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