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

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Basic information

Entry
Database: PDB / ID: 8alh
TitleX-ray structure of human NCS-1 bound to Ric-8A
Components
  • Neuronal calcium sensor 1
  • Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)
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 / voltage-gated calcium channel activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / guanyl-nucleotide exchange factor activity ...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 / voltage-gated calcium channel activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / guanyl-nucleotide exchange factor activity / visual learning / in utero embryonic development / postsynaptic density / axon / intracellular membrane-bounded organelle / dendrite / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / plasma membrane / cytoplasm
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
Synembryn / Neuronal calcium sensor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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
DepositionAug 1, 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: Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,60111
Polymers23,6322
Non-polymers9709
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, The assembly was verified by nano-DSF and crystallization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-77 kcal/mol
Surface area10730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.861, 56.861, 134.612
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-359-

HOH

31B-386-

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 Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans) / Ric8a protein / Synembryn-A


Mass: 3088.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: B1H241

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Non-polymers , 7 types, 150 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 / Polyethylene glycol


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


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


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


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 30 % PEG 4000, 100 mM sodium acetate pH 4.6, 100 mM magnesium chloride
PH range: 4.8-5.0

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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: Nov 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979263 Å / Relative weight: 1
ReflectionResolution: 1.854→52.38 Å / Num. obs: 18029 / % possible obs: 94 % / Redundancy: 8.7 % / CC1/2: 0.999 / Net I/σ(I): 15.2
Reflection shellResolution: 1.854→1.942 Å / Num. unique obs: 881 / CC1/2: 0.467

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
PDB_EXTRACT3.27data extraction
AutoProcess1.0.5data reduction
PHASERphasing
Aimless0.7.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QI4

6qi4


Resolution: 1.86→52.38 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 843 4.68 %
Rwork0.1958 --
obs0.1975 18029 92.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→52.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1605 0 25 141 1771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091703
X-RAY DIFFRACTIONf_angle_d0.922293
X-RAY DIFFRACTIONf_dihedral_angle_d8.844238
X-RAY DIFFRACTIONf_chiral_restr0.052239
X-RAY DIFFRACTIONf_plane_restr0.008301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.970.2849760.26311687X-RAY DIFFRACTION56
1.97-2.120.26141370.24373003X-RAY DIFFRACTION99
2.12-2.340.27071490.19073036X-RAY DIFFRACTION100
2.34-2.680.23681560.1963062X-RAY DIFFRACTION100
2.68-3.370.23451470.18763119X-RAY DIFFRACTION100
3.37-52.380.21451780.18933279X-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)
12.26313.98042.83064.92140.89316.5963-0.10411.01581.60360.70940.3888-0.6535-1.4731.5818-0.21690.5874-0.09070.02490.4615-0.05180.782-0.080639.038220.9483
23.75580.68850.24942.68290.86373.6718-0.1277-0.50110.1210.32490.0087-0.1440.2050.2220.10210.19070.01520.00390.31890.0010.17551.397123.104327.497
33.3895-0.13770.16154.05421.76231.8818-0.1160.17550.131-0.00480.1214-0.2188-0.00590.2598-0.01230.21780.00240.010.29160.03510.1963.183820.489218.097
42.7855-0.9946-0.722.79731.53082.1737-0.1167-0.1449-0.66180.1417-0.02130.3860.39090.03770.09610.23080.00340.04680.17450.03660.3044-2.70635.531411.4785
55.14521.549-1.84894.55530.79945.3639-0.09250.8077-0.89-0.1925-0.10640.93180.2728-0.63740.12120.2623-0.0139-0.07880.3569-0.08290.4846-8.756.10362.3106
62.90011.8447-2.34461.1506-1.48541.90720.1861-0.5053-0.04680.08350.150.8837-0.8751-0.9935-0.41621.861-0.2821-0.07330.94890.29821.1752-14.49165.583622.9541
72.04121.2295-3.10047.76410.8973.2139-0.1696-0.3212-0.47790.2865-0.31380.32660.65860.06590.42560.26380.00180.06420.2326-0.01570.2992-11.00946.84413.801
85.254.83555.32082.5128.88522.2592-0.1258-0.58570.41530.4535-0.50480.75570.5401-0.41990.48180.2997-0.00880.03870.27910.02260.2811-4.665917.202523.4961
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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