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

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Basic information

Entry
Database: PDB / ID: 8alm
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 / response to light stimulus / G-protein alpha-subunit binding / 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 / response to light stimulus / G-protein alpha-subunit binding / voltage-gated calcium channel activity / gastrulation / GTPase activator activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / guanyl-nucleotide exchange factor activity / visual learning / in utero embryonic development / postsynaptic density / G protein-coupled receptor signaling pathway / axon / intracellular membrane-bounded organelle / dendrite / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / membrane / 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
Neuronal calcium sensor 1 / Synembryn-A
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85402 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: Synembryn-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6229
Polymers23,9152
Non-polymers7077
Water2,090116
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 area3640 Å2
ΔGint-71 kcal/mol
Surface area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.639, 56.639, 134.532
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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 , 6 types, 123 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-1PE / PENTAETHYLENE GLYCOL / PEG400


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


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


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


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 30 % PEG 4000, 100 mM sodium acetate pH 4.6

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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: 1.85402→52.2013 Å / Num. obs: 17666 / % possible obs: 91.11 % / Redundancy: 8.7 % / CC1/2: 0.999 / Net I/σ(I): 15.2
Reflection shellResolution: 1.85402→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
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.85402→52.2 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 827 4.68 %
Rwork0.2098 --
obs0.2118 17665 91.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85402→52.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1605 0 20 116 1741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111676
X-RAY DIFFRACTIONf_angle_d1.1362254
X-RAY DIFFRACTIONf_dihedral_angle_d8.393230
X-RAY DIFFRACTIONf_chiral_restr0.054235
X-RAY DIFFRACTIONf_plane_restr0.013295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85402-1.970.4621690.36891431X-RAY DIFFRACTION48
1.97-2.120.31191310.26622980X-RAY DIFFRACTION98
2.12-2.340.30041480.20463015X-RAY DIFFRACTION100
2.34-2.670.3051560.22353060X-RAY DIFFRACTION100
2.67-3.370.23541460.20883093X-RAY DIFFRACTION100
3.37-52.20.22761770.19523259X-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)
19.88793.02113.40815.73982.17195.91330.261-0.15932.14780.4089-0.0484-0.9357-1.52681.2537-0.07780.6222-0.14670.09780.4239-0.13040.83560.067138.846621.0041
24.94240.80840.60512.58351.36384.1389-0.0253-1.1412-0.04660.5298-0.0662-0.09880.33420.12630.09760.2973-0.02330.03880.48740.02540.23281.35622.962627.4997
34.1097-0.19110.30663.49422.20721.9125-0.05250.06170.06420.0150.0826-0.29480.04910.3397-0.06240.2135-0.00320.01990.26520.04850.17383.149520.311718.0935
43.3245-0.27830.04154.21221.98871.52580.0444-0.1224-0.78590.0044-0.10060.02760.34010.04010.10390.28810.01490.04450.2160.04280.3723-2.57465.859211.328
54.97060.9339-1.75234.10490.26285.8143-0.15040.6531-0.8027-0.3067-0.03291.03510.3972-0.83190.16030.3596-0.0283-0.05380.4028-0.06620.534-8.85146.0592.2913
62.75091.3697-2.97510.661-1.4733.2429-0.1061-0.4393-0.14370.5048-0.2390.32850.1554-0.37040.35461.0134-0.0503-0.18191.50790.07541.0282-14.49585.507322.9999
72.04160.9717-2.79065.78552.2992.079-0.3824-0.3305-0.59070.17220.210.29410.96930.13980.33580.34770.01630.08250.2480.03660.4284-11.07826.741313.8072
85.27743.70323.54542.51377.37872.1805-0.2124-0.93480.33940.5651-0.56780.91350.5227-0.33270.35720.39790.00020.05760.36260.02240.3403-4.77217.051423.4927
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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