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- PDB-8c3r: Crystal structure of DYRK1A in complex with gossypin -

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Basic information

Entry
Database: PDB / ID: 8c3r
TitleCrystal structure of DYRK1A in complex with gossypin
ComponentsDual specificity tyrosine-phosphorylation-regulated kinase 1A
KeywordsTRANSFERASE / Kinase / diabetes / kinase inhibitor
Function / homology
Function and homology information


negative regulation of heterochromatin formation / peptidyl-serine autophosphorylation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / tau-protein kinase activity / negative regulation of microtubule polymerization / negative regulation of DNA damage response, signal transduction by p53 class mediator / amyloid-beta formation / negative regulation of mRNA splicing, via spliceosome / G0 and Early G1 ...negative regulation of heterochromatin formation / peptidyl-serine autophosphorylation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / tau-protein kinase activity / negative regulation of microtubule polymerization / negative regulation of DNA damage response, signal transduction by p53 class mediator / amyloid-beta formation / negative regulation of mRNA splicing, via spliceosome / G0 and Early G1 / peptidyl-tyrosine autophosphorylation / cytoskeletal protein binding / RNA polymerase II CTD heptapeptide repeat kinase activity / peptidyl-threonine phosphorylation / protein serine/threonine/tyrosine kinase activity / tubulin binding / positive regulation of RNA splicing / non-membrane spanning protein tyrosine kinase activity / peptidyl-tyrosine phosphorylation / tau protein binding / circadian rhythm / nervous system development / peptidyl-serine phosphorylation / actin binding / protein autophosphorylation / protein tyrosine kinase activity / transcription coactivator activity / histone H3T45 kinase activity / protein kinase activity / nuclear speck / protein phosphorylation / axon / ribonucleoprotein complex / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / dendrite / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / 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
ACETATE ION / Gossypin / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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 gossypin
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
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)87,5588
Polymers86,3612
Non-polymers1,1976
Water7,566420
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A: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7203
Polymers43,1811
Non-polymers5392
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)43,8385
Polymers43,1811
Non-polymers6584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.126, 132.126, 90.485
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 / 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-R7O / Gossypin / 2-[3,4-bis(oxidanyl)phenyl]-8-[(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,5,7-tris(oxidanyl)chromen-4-one / 2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-8-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxychromen-4-one


Mass: 480.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H20O13 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 53.41 %
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: BESSY / Beamline: 14.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→48.36 Å / Num. obs: 55250 / % possible obs: 99.4 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.027 / Rrim(I) all: 0.098 / Χ2: 1.01 / Net I/σ(I): 18.6 / Num. measured all: 719290
Reflection shellResolution: 2.06→2.12 Å / % possible obs: 95.9 % / Redundancy: 9.3 % / Rmerge(I) obs: 1.519 / Num. measured all: 38380 / Num. unique obs: 4133 / CC1/2: 0.518 / Rpim(I) all: 0.516 / Rrim(I) all: 1.607 / Χ2: 1.01 / 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: 2.06→48.36 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 2763 5 %
Rwork0.1855 --
obs0.1867 55222 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5521 0 84 420 6025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055757
X-RAY DIFFRACTIONf_angle_d0.7037806
X-RAY DIFFRACTIONf_dihedral_angle_d15.422148
X-RAY DIFFRACTIONf_chiral_restr0.048836
X-RAY DIFFRACTIONf_plane_restr0.0041051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.10.33481340.29792497X-RAY DIFFRACTION95
2.1-2.130.31821160.27692575X-RAY DIFFRACTION97
2.13-2.170.34521300.25462567X-RAY DIFFRACTION98
2.17-2.220.26951340.25022577X-RAY DIFFRACTION98
2.22-2.270.27651500.23942620X-RAY DIFFRACTION100
2.27-2.320.27151320.22622645X-RAY DIFFRACTION100
2.32-2.380.26391290.2232596X-RAY DIFFRACTION100
2.38-2.440.2561090.2122661X-RAY DIFFRACTION100
2.44-2.510.25331330.22062646X-RAY DIFFRACTION100
2.51-2.590.26751550.20792606X-RAY DIFFRACTION100
2.6-2.690.23391490.21792629X-RAY DIFFRACTION100
2.69-2.80.2331500.21082639X-RAY DIFFRACTION100
2.8-2.920.26331420.22692613X-RAY DIFFRACTION100
2.92-3.080.22581540.20582640X-RAY DIFFRACTION100
3.08-3.270.22151420.19022631X-RAY DIFFRACTION100
3.27-3.520.21031350.17842621X-RAY DIFFRACTION100
3.52-3.880.18771070.15862698X-RAY DIFFRACTION100
3.88-4.440.15121580.13982640X-RAY DIFFRACTION100
4.44-5.590.16511590.15122642X-RAY DIFFRACTION100
5.59-48.360.17591450.16662716X-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)
13.4089-0.91040.75574.0433-0.31593.17310.0397-0.2858-0.26970.28140.02440.0032-0.0176-0.1709-0.05560.3348-0.081-0.02290.25590.02010.268-29.3148-6.768327.8903
23.0907-0.62822.33425.33740.08131.82290.00650.3095-0.4123-0.3607-0.0901-0.67420.13210.12210.0410.20690.01270.02620.2014-0.05540.3775-24.2399-7.255420.2897
31.91250.52240.04281.792-0.18241.35020.02290.17260.1230.0079-0.00780.1052-0.0015-0.2076-0.00440.18330.01420.04530.29080.00620.1732-24.614819.565912.792
43.0584-0.8349-0.64595.4927-1.86923.08650.09320.1276-0.10310.33790.25110.6736-0.3997-0.4032-0.31940.53170.17870.06730.35980.08420.5195-48.437558.699424.894
54.0147-0.62010.03493.2027-0.15562.26380.1003-0.18160.13980.5729-0.1371-0.269-0.6365-0.01260.01750.58040.0497-0.05650.25420.05480.3356-32.578750.350132.9904
61.19180.2874-0.67571.6212-0.75961.8560.0083-0.3408-0.52550.4478-0.2695-0.6461-0.28480.26520.23470.44410.0224-0.14120.34380.14480.5893-28.267333.675538.6535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 135 through 213 )
2X-RAY DIFFRACTION2chain 'A' and (resid 214 through 239 )
3X-RAY DIFFRACTION3chain 'A' and (resid 240 through 480 )
4X-RAY DIFFRACTION4chain 'B' and (resid 136 through 239 )
5X-RAY DIFFRACTION5chain 'B' and (resid 240 through 320 )
6X-RAY DIFFRACTION6chain 'B' and (resid 322 through 480 )

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