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- PDB-8ahy: X-ray structure of human NCS-1 bound to Ric-8A -

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Basic information

Entry
Database: PDB / ID: 8ahy
TitleX-ray structure of human NCS-1 bound to Ric-8A
Components
  • Neuronal calcium sensor 1
  • Synembryn-A
KeywordsSTRUCTURAL PROTEIN / NCS-1 / Ric-8A / complex
Function / homology
Function and homology information


cell-cell adhesion involved in gastrulation / calcium sensitive guanylate cyclase activator activity / cell migration involved in gastrulation / basement membrane organization / vasculature development / regulation of neuron projection development / G-protein alpha-subunit binding / response to light stimulus / voltage-gated calcium channel activity / gastrulation ...cell-cell adhesion involved in gastrulation / calcium sensitive guanylate cyclase activator activity / cell migration involved in gastrulation / basement membrane organization / vasculature development / regulation of neuron projection development / G-protein alpha-subunit binding / response to light stimulus / voltage-gated calcium channel activity / gastrulation / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / GTPase activator activity / guanyl-nucleotide exchange factor activity / visual learning / in utero embryonic development / postsynaptic density / G protein-coupled receptor signaling pathway / axon / intracellular membrane-bounded organelle / calcium ion binding / dendrite / perinuclear region of cytoplasm / Golgi apparatus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Synembryn / Guanine nucleotide exchange factor, Ric8 / Guanine nucleotide exchange factor synembryn / 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. ...Synembryn / Guanine nucleotide exchange factor, Ric8 / Guanine nucleotide exchange factor synembryn / 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 / Armadillo-like helical / EF-hand domain pair / Armadillo-type fold
Similarity search - Domain/homology
Neuronal calcium sensor 1 / Synembryn-A
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsMunoz-Reyes, D. / Sanchez-Barrena, M.J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2019-111737RB-I00 Spain
CitationJournal: Elife / Year: 2023
Title: The neuronal calcium sensor NCS-1 regulates the phosphorylation state and activity of the G alpha chaperone and GEF Ric-8A.
Authors: Munoz-Reyes, D. / McClelland, L.J. / Arroyo-Urea, S. / Sanchez-Yepes, S. / Sabin, J. / Perez-Suarez, S. / Menendez, M. / Mansilla, A. / Garcia-Nafria, J. / Sprang, S. / Sanchez-Barrena, M.J.
History
DepositionJul 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation / Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Neuronal calcium sensor 1
P: Synembryn-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,64610
Polymers23,9152
Non-polymers7328
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.635, 56.635, 135.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-204-

MG

21B-355-

HOH

31B-392-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules BP

#1: Protein Neuronal calcium sensor 1 / NCS-1 / Frequenin homolog / Frequenin-like protein / Frequenin-like ubiquitous protein


Mass: 20543.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCS1, FLUP, FREQ / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P62166
#2: Protein/peptide Synembryn-A / Protein Ric-8A


Mass: 3371.826 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q80ZG1

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Non-polymers , 7 types, 152 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30 % PEG 4000, 100 mM sodium acetate pH 4.6, 100 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979263 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979263 Å / Relative weight: 1
ReflectionResolution: 1.7→52.24 Å / Num. obs: 44184 / % possible obs: 96 % / Redundancy: 25.5 % / CC1/2: 0.997 / Net I/σ(I): 13.6
Reflection shellResolution: 1.704→1.784 Å / Num. unique obs: 1101 / CC1/2: 0.538 / % possible all: 66.4

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
PDB_EXTRACT3.27data extraction
autoPROC1.0.5data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→52.24 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 23.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 1958 4.83 %
Rwork0.1864 --
obs0.1874 40563 88.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→52.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1605 0 21 144 1770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071676
X-RAY DIFFRACTIONf_angle_d0.7742254
X-RAY DIFFRACTIONf_dihedral_angle_d8.626230
X-RAY DIFFRACTIONf_chiral_restr0.052235
X-RAY DIFFRACTIONf_plane_restr0.007295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.45260.3465598X-RAY DIFFRACTION19
1.75-1.790.3022970.32331809X-RAY DIFFRACTION59
1.79-1.850.30951160.29832324X-RAY DIFFRACTION74
1.85-1.910.24121470.26792743X-RAY DIFFRACTION88
1.91-1.970.28371700.24683017X-RAY DIFFRACTION98
1.97-2.050.23671480.22143113X-RAY DIFFRACTION100
2.05-2.150.19851430.22223141X-RAY DIFFRACTION100
2.15-2.260.18431520.17233165X-RAY DIFFRACTION100
2.26-2.40.22891690.18173072X-RAY DIFFRACTION100
2.4-2.590.15171400.17123172X-RAY DIFFRACTION100
2.59-2.850.21821720.18133101X-RAY DIFFRACTION100
2.85-3.260.1961730.17983092X-RAY DIFFRACTION100
3.26-4.110.17951600.15543122X-RAY DIFFRACTION100
4.11-52.240.21751450.18023136X-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)
18.20912.18632.27443.46840.95714.7932-0.08480.48021.91040.36790.0883-1.1058-0.52230.65860.12910.3542-0.0562-0.05150.2678-0.09680.77070.054238.752921.2783
23.13870.37160.15311.17610.55862.17-0.1006-0.6191-0.00910.33080.0348-0.09250.28430.20590.08740.21950.03640.0120.3263-0.00320.14121.355722.784527.7063
32.1652-0.20760.30232.1991.48661.506-0.0639-0.05850.15250.07370.1349-0.15310.10140.2167-0.05680.15110.01220.01860.19230.00730.1453.186120.171818.2735
41.8483-0.1695-0.05861.54220.64110.7024-0.0064-0.1172-0.43890.1636-0.06660.16330.140.06520.05410.18810.00350.04030.15080.02450.2101-2.57375.865211.313
52.94070.6554-1.08362.59580.47243.5323-0.10060.2717-0.26770.0622-0.07330.70640.3468-0.56190.1530.1966-0.03850.00060.2732-0.0450.3387-8.78966.05552.2608
62.32041.8175-2.32061.4037-1.80912.329-0.3287-0.411-0.32990.5932-0.14570.42580.1466-0.4540.20281.02190.1294-0.0870.92790.07451.2475-14.6125.412722.6225
77.68350.2295-1.28013.00031.5471.5546-0.2751-0.5447-0.39380.09060.04320.16390.47450.06870.14380.2246-0.00180.0790.18220.00210.2029-11.05356.717113.7286
82.89161.89961.35317.13154.74157.7407-0.0929-0.5570.18480.8673-0.23460.57670.4936-0.20620.23770.25780.01780.06960.22890.00760.2281-4.840216.92423.5815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 6 through 19 )
2X-RAY DIFFRACTION2chain 'B' and (resid 20 through 58 )
3X-RAY DIFFRACTION3chain 'B' and (resid 59 through 96 )
4X-RAY DIFFRACTION4chain 'B' and (resid 97 through 144 )
5X-RAY DIFFRACTION5chain 'B' and (resid 145 through 176 )
6X-RAY DIFFRACTION6chain 'P' and (resid 402 through 406 )
7X-RAY DIFFRACTION7chain 'P' and (resid 407 through 413 )
8X-RAY DIFFRACTION8chain 'P' and (resid 414 through 429 )

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