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- PDB-8c3q: Crystal structure of DYRK1A in complex with rutin -

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Basic information

Entry
Database: PDB / ID: 8c3q
TitleCrystal structure of DYRK1A in complex with rutin
ComponentsDual specificity tyrosine-phosphorylation-regulated kinase 1ADYRK1A
KeywordsTRANSFERASE / Kinase / diabetes / kinase inhibitor
Function / homology
Function and homology information


histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of mRNA splicing, via spliceosome ...histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of mRNA splicing, via spliceosome / amyloid-beta formation / G0 and Early G1 / peptidyl-tyrosine autophosphorylation / cytoskeletal protein binding / protein serine/threonine/tyrosine kinase activity / tubulin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / positive regulation of RNA splicing / peptidyl-threonine phosphorylation / non-membrane spanning protein tyrosine kinase activity / tau protein binding / circadian rhythm / peptidyl-tyrosine phosphorylation / : / nervous system development / actin binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / protein autophosphorylation / transcription coactivator activity / cytoskeleton / protein kinase activity / nuclear speck / ribonucleoprotein complex / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
RUTIN / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsGrygier, P. / Pustelny, K. / Dubin, G. / Czarna, A.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science Centre2019/34/E/NZ1/00467 Poland
National Center for Research and Development (Poland)PPN/PPO/2018/1/00046 Poland
CitationJournal: To Be Published
Title: Crystal structure of DYRK1A in complex with rutin
Authors: Grygier, P. / Pustelny, K. / Dubin, G. / Czarna, A.
History
DepositionDec 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
B: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5824
Polymers86,3612
Non-polymers1,2212
Water3,423190
1
A: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7912
Polymers43,1811
Non-polymers6111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7912
Polymers43,1811
Non-polymers6111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.187, 134.187, 91.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Dual specificity tyrosine-phosphorylation-regulated kinase 1A / DYRK1A / Dual specificity YAK1-related kinase / HP86 / Protein kinase minibrain homolog / MNBH / hMNB


Mass: 43180.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK1A, DYRK, MNB, MNBH / Production host: Escherichia coli (E. coli) / References: UniProt: Q13627, dual-specificity kinase
#2: Chemical ChemComp-RUT / RUTIN / 2-(3,4-DIHYDROXYPHENYL)-5,7-DIHYDROXY-4-OXO-4H-CHROMEN-3-YL 6-O-(6-DEOXY-ALPHA-L-MANNOPYRANOSYL)-BETA-D-GLUCOPYRANOSIDE / Rutin


Mass: 610.517 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H30O16 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 5.5, 0.2 M ammonium acetate, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.32→49 Å / Num. obs: 40460 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.042 / Rrim(I) all: 0.116 / Χ2: 1.02 / Net I/σ(I): 12.4 / Num. measured all: 296199
Reflection shellResolution: 2.32→2.4 Å / % possible obs: 100 % / Redundancy: 7.6 % / Rmerge(I) obs: 1.618 / Num. measured all: 29984 / Num. unique obs: 3951 / CC1/2: 0.487 / Rpim(I) all: 0.624 / Rrim(I) all: 1.736 / Χ2: 1.07 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.20.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EIS

6eis


Resolution: 2.32→49 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 2006 4.96 %
Rwork0.1769 --
obs0.1785 40432 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5465 0 86 190 5741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075696
X-RAY DIFFRACTIONf_angle_d0.897730
X-RAY DIFFRACTIONf_dihedral_angle_d15.5562118
X-RAY DIFFRACTIONf_chiral_restr0.055842
X-RAY DIFFRACTIONf_plane_restr0.0071028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.380.32141460.29752706X-RAY DIFFRACTION100
2.38-2.440.32641480.26782724X-RAY DIFFRACTION100
2.44-2.510.27371550.25162697X-RAY DIFFRACTION100
2.51-2.60.24921510.23922737X-RAY DIFFRACTION100
2.6-2.690.27981370.22062756X-RAY DIFFRACTION100
2.69-2.80.26461270.22512775X-RAY DIFFRACTION100
2.8-2.920.27851550.21912703X-RAY DIFFRACTION100
2.92-3.080.26171640.2192724X-RAY DIFFRACTION100
3.08-3.270.26271290.19042752X-RAY DIFFRACTION100
3.27-3.520.20641200.18472796X-RAY DIFFRACTION100
3.52-3.880.21441010.15642765X-RAY DIFFRACTION100
3.88-4.440.16581620.13832746X-RAY DIFFRACTION100
4.44-5.590.17561680.14332752X-RAY DIFFRACTION100
5.59-490.16291430.15342793X-RAY DIFFRACTION99
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)
14.60750.8571-0.5753.9562-1.16814.87960.2154-0.1395-0.44010.3546-0.05690.10670.0415-0.2106-0.12760.3254-0.0098-0.04870.25340.0050.4073-28.3189-6.838425.5114
23.84781.5296-0.44175.2619-0.84182.45840.15540.1314-0.11830.2539-0.0825-0.1243-0.00690.0284-0.07770.26640.04190.00210.34730.02050.1994-20.19899.413716.7506
32.46081.02840.18013.1808-0.34891.95440.02730.5670.7184-0.18860.04590.5964-0.1405-0.15040.01770.29720.06330.01140.47040.14650.436-26.112624.778210.3158
48.0650.3829-1.166.8538-3.98638.3968-0.05950.7417-0.4553-1.29780.69341.16830.8091-1.7617-0.56720.71330.0189-0.15030.83790.08470.6569-55.789258.158115.4631
53.25460.1927-0.67095.7922-1.48793.81050.09550.1490.0856-0.46260.0056-0.0417-0.2126-0.2935-0.16730.65390.1557-0.00740.39240.03880.4713-45.939860.679619.7468
63.3207-0.7277-0.09184.727-1.27763.6504-0.2461-0.20640.3080.36760.33160.141-0.4399-0.4623-0.1440.7240.1850.05810.39120.03610.5026-45.60859.556530.953
73.9137-0.6278-0.01943.9211-0.1963.27570.0292-0.0391-0.02970.1456-0.0801-0.5988-0.47570.2048-0.00680.65670.10310.0140.31980.04850.5016-28.710451.158331.4671
83.6289-1.43291.78772.16551.00793.59920.0635-0.3962-0.28120.5274-0.27990.5220.1531-0.98720.03790.78540.13880.16970.53480.04790.5767-43.24649.478137.4371
91.71751.0328-0.02014.8952-0.59941.67740.1152-0.3456-0.34230.6064-0.1782-0.3104-0.1893-0.08620.07640.56220.1305-0.04120.41360.10470.4855-34.33132.55338.0276
102.79471.2319-2.21241.1951-0.49653.11640.0116-0.1626-0.30180.4961-0.1268-0.80850.20840.08010.12230.69040.1727-0.10.44490.1130.8989-23.376325.839833.2268
112.5485-0.8301-0.02394.77430.51663.022-0.0322-0.42880.06230.58080.1657-1.1518-0.40660.5216-0.10190.74680.0586-0.18880.49480.01150.7044-19.9443.67140.8727
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 134 through 239 )
2X-RAY DIFFRACTION2chain 'A' and (resid 240 through 320 )
3X-RAY DIFFRACTION3chain 'A' and (resid 322 through 480 )
4X-RAY DIFFRACTION4chain 'B' and (resid 136 through 158 )
5X-RAY DIFFRACTION5chain 'B' and (resid 159 through 193 )
6X-RAY DIFFRACTION6chain 'B' and (resid 194 through 244 )
7X-RAY DIFFRACTION7chain 'B' and (resid 245 through 302 )
8X-RAY DIFFRACTION8chain 'B' and (resid 303 through 320 )
9X-RAY DIFFRACTION9chain 'B' and (resid 322 through 402 )
10X-RAY DIFFRACTION10chain 'B' and (resid 403 through 436 )
11X-RAY DIFFRACTION11chain 'B' and (resid 437 through 480 )

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