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- PDB-6qi4: NCS-1 bound to a ligand -

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Basic information

Entry
Database: PDB / ID: 6qi4
TitleNCS-1 bound to a ligand
ComponentsNeuronal calcium sensor 1
KeywordsMETAL BINDING PROTEIN / Calcium sensor / synapse regulation
Function / homology
Function and homology information


calcium sensitive guanylate cyclase activator activity / regulation of neuron projection development / voltage-gated calcium channel activity / postsynaptic density / axon / intracellular membrane-bounded organelle / dendrite / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus ...calcium sensitive guanylate cyclase activator activity / regulation of neuron projection development / voltage-gated calcium channel activity / postsynaptic density / axon / intracellular membrane-bounded organelle / dendrite / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / plasma membrane / cytoplasm
Similarity search - Function
Recoverin family / EF hand / 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
Similarity search - Domain/homology
ACETATE ION / Chem-FKW / Neuronal calcium sensor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsSanchez-Barrena, M.J. / Blanco-Gabella, P.
CitationJournal: Nat Commun / Year: 2019
Title: Insights into real-time chemical processes in a calcium sensor protein-directed dynamic library.
Authors: Canal-Martin, A. / Sastre, J. / Sanchez-Barrena, M.J. / Canales, A. / Baldominos, S. / Pascual, N. / Martinez-Gonzalez, L. / Molero, D. / Fernandez-Valle, M.E. / Saez, E. / Blanco-Gabella, P. ...Authors: Canal-Martin, A. / Sastre, J. / Sanchez-Barrena, M.J. / Canales, A. / Baldominos, S. / Pascual, N. / Martinez-Gonzalez, L. / Molero, D. / Fernandez-Valle, M.E. / Saez, E. / Blanco-Gabella, P. / Gomez-Rubio, E. / Martin-Santamaria, S. / Saiz, A. / Mansilla, A. / Canada, F.J. / Jimenez-Barbero, J. / Martinez, A. / Perez-Fernandez, R.
History
DepositionJan 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_auth_asym_id / _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_asym_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_symmetry
Revision 1.2Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Neuronal calcium sensor 1
C: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,32320
Polymers43,8052
Non-polymers2,51818
Water3,081171
1
B: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,75713
Polymers21,9031
Non-polymers1,85412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5677
Polymers21,9031
Non-polymers6646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.729, 55.603, 77.725
Angle α, β, γ (deg.)90.00, 94.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules BC

#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.) Homo sapiens (human) / Gene: NCS1, FLUP, FREQ / Production host: Escherichia coli (E. coli) / References: UniProt: P62166

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Non-polymers , 8 types, 189 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Chemical ChemComp-FKW / 2-(1~{H}-indol-3-yl)-~{N}-[(~{E})-(4-nitro-3-oxidanyl-phenyl)methylideneamino]ethanamide


Mass: 338.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N4O4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate trihydrate pH 6.5, 0.2 M sodium acetate trihydrate, 30% (v/v) polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.978979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978979 Å / Relative weight: 1
ReflectionResolution: 1.78→42.35 Å / Num. obs: 43813 / % possible obs: 99.6 % / Redundancy: 3.4 % / Rpim(I) all: 0.045 / Net I/σ(I): 8.5
Reflection shellResolution: 1.78→1.8 Å / Rpim(I) all: 1.129

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: 000)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1g8i

1g8i


Resolution: 1.78→42.347 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 30.36
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 4356 5.25 %random
Rwork0.2135 ---
obs0.2145 83021 96.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.78→42.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 122 171 3331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143229
X-RAY DIFFRACTIONf_angle_d1.3034318
X-RAY DIFFRACTIONf_dihedral_angle_d17.7641955
X-RAY DIFFRACTIONf_chiral_restr0.063445
X-RAY DIFFRACTIONf_plane_restr0.01581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.80020.40841290.3892668X-RAY DIFFRACTION96
1.8002-1.82140.4171520.38062502X-RAY DIFFRACTION94
1.8214-1.84360.40461270.36972621X-RAY DIFFRACTION94
1.8436-1.8670.39071370.3582579X-RAY DIFFRACTION97
1.867-1.89150.39841410.35382651X-RAY DIFFRACTION96
1.8915-1.91740.35821380.33612646X-RAY DIFFRACTION97
1.9174-1.94480.3481230.32992613X-RAY DIFFRACTION97
1.9448-1.97390.35551430.31232598X-RAY DIFFRACTION96
1.9739-2.00470.33641350.31332650X-RAY DIFFRACTION98
2.0047-2.03760.28841380.29022710X-RAY DIFFRACTION98
2.0376-2.07270.32951460.27632578X-RAY DIFFRACTION97
2.0727-2.11040.30291600.2662626X-RAY DIFFRACTION97
2.1104-2.1510.25161660.25792583X-RAY DIFFRACTION95
2.151-2.19490.27941680.22662454X-RAY DIFFRACTION93
2.1949-2.24260.28741360.22622695X-RAY DIFFRACTION97
2.2426-2.29480.20421500.21422593X-RAY DIFFRACTION97
2.2948-2.35220.24391510.2122680X-RAY DIFFRACTION97
2.3522-2.41580.19361340.21212659X-RAY DIFFRACTION97
2.4158-2.48680.25351460.20492619X-RAY DIFFRACTION98
2.4868-2.56710.23841750.21342687X-RAY DIFFRACTION98
2.5671-2.65880.22511390.20022650X-RAY DIFFRACTION97
2.6588-2.76530.26651300.20962549X-RAY DIFFRACTION95
2.7653-2.89110.24621120.19842632X-RAY DIFFRACTION96
2.8911-3.04350.19751660.20982593X-RAY DIFFRACTION97
3.0435-3.23410.20761570.2192664X-RAY DIFFRACTION97
3.2341-3.48370.24791400.20082673X-RAY DIFFRACTION99
3.4837-3.83410.23571550.18762624X-RAY DIFFRACTION97
3.8341-4.38840.20351510.16922549X-RAY DIFFRACTION95
4.3884-5.5270.15041750.17612672X-RAY DIFFRACTION98
5.527-42.3590.20861360.18872647X-RAY DIFFRACTION98
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)
10.4209-0.34120.02933.34550.6610.42920.08250.11080.0632-0.2612-0.0945-0.377-0.050.01070.01560.14240.01370.03030.24370.02680.265-13.3556-13.1534-3.1939
20.70630.23690.13912.694-0.35551.5040.0162-0.0074-0.0283-0.07020.04090.24020.3497-0.01360.00270.5144-0.0181-0.06260.24490.00670.2297-8.1926-23.300225.4847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 3 through 189)
2X-RAY DIFFRACTION2(chain 'C' and resid 3 through 188)

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