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- PDB-7z5n: Crystal structure of DYRK1A in complex with CX-4945 -

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Basic information

Entry
Database: PDB / ID: 7z5n
TitleCrystal structure of DYRK1A in complex with CX-4945
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
Chem-3NG / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsPustelny, K. / Grygier, P. / Golik, P. / 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 DYRK1A in complex with CX-4945
Authors: Grygier, P. / Pustelny, K. / Golik, P. / Popowicz, G. / Dubin, G. / Czarna, A.
History
DepositionMar 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
D: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
E: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
F: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
G: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
H: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,44265
Polymers345,4458
Non-polymers7,99757
Water3,711206
1
A: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,69113
Polymers43,1811
Non-polymers1,51112
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)44,73513
Polymers43,1811
Non-polymers1,55512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1999
Polymers43,1811
Non-polymers1,0188
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0136
Polymers43,1811
Non-polymers8325
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0857
Polymers43,1811
Non-polymers9046
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6884
Polymers43,1811
Non-polymers5083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0598
Polymers43,1811
Non-polymers8787
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9715
Polymers43,1811
Non-polymers7904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)247.682, 134.317, 121.717
Angle α, β, γ (deg.)90.000, 96.480, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#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.: 8
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) / Strain (production host): LOBSTR / References: UniProt: Q13627, dual-specificity kinase

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Non-polymers , 7 types, 263 molecules

#2: Chemical
ChemComp-3NG / 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid / Silmitasertib


Mass: 349.770 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C19H12ClN3O2 / Comment: chemotherapy, inhibitor*YM
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0,1M TRIS pH 7.7, 0,1M Li2SO4, 40% PEG300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.77→48.11 Å / Num. obs: 100435 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 71.87 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.06 / Rrim(I) all: 0.119 / Net I/σ(I): 10.5 / Num. measured all: 385861 / Scaling rejects: 72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.77-2.823.91.6851965749790.340.9651.9470.999.9
15.17-48.113.10.03518125800.9970.0250.04326.990.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EIS

6eis


Resolution: 2.77→26.14 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2516 5108 5.09 %
Rwork0.205 95182 -
obs0.2073 100290 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 247.92 Å2 / Biso mean: 84.9253 Å2 / Biso min: 37.69 Å2
Refinement stepCycle: final / Resolution: 2.77→26.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21206 0 514 206 21926
Biso mean--82.1 67.82 -
Num. residues----2697
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.77-2.80.39191700.343531263296100
2.8-2.830.41471700.327231803350100
2.83-2.870.36431630.308931713334100
2.87-2.910.34491610.311631373298100
2.91-2.940.33431720.297731823354100
2.94-2.980.34111660.295931903356100
2.98-3.030.33641620.291931443306100
3.03-3.070.35611910.291931433334100
3.07-3.120.31661700.275631983368100
3.12-3.170.30991550.261431433298100
3.17-3.220.29191620.259131513313100
3.22-3.280.33881870.255732043391100
3.28-3.350.3041840.241431283312100
3.35-3.410.30721640.236331663330100
3.41-3.490.2781900.223631623352100
3.49-3.570.27381460.223831873333100
3.57-3.660.27941780.202531683346100
3.66-3.760.22131640.194531823346100
3.76-3.870.23281860.182731353321100
3.87-3.990.25111730.176631953368100
3.99-4.130.2371520.179232113363100
4.13-4.30.24131590.169831633322100
4.3-4.490.18971680.156331523320100
4.49-4.730.19141720.156731933365100
4.73-5.020.20591750.167931853360100
5.02-5.410.23791740.187431823356100
5.41-5.950.24332060.209431353341100
5.95-6.790.24711790.214832073386100
6.79-8.510.25181450.185932443389100
8.51-26.140.19431640.18353218338298
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)
12.47320.40351.5912.97780.47675.8322-0.36010.00510.46540.18280.2226-0.3968-0.61410.4970.13330.4873-0.0385-0.09360.39750.01540.475364.217335.332964.9775
23.5522-0.52111.27072.17290.2645.3309-0.10370.32850.26230.06150.0731-0.2864-0.22690.31240.05090.5079-0.08610.04330.3493-0.01220.404455.848328.918448.8886
33.7923-0.1834-0.25411.5603-0.35733.6726-0.121-0.1619-0.38680.25510.03960.38570.4298-0.21070.11690.5813-0.09190.11190.3266-0.0640.442940.450818.651750.4545
43.56110.48360.36144.3908-1.083.5636-0.19340.33-0.46090.05980.09210.76590.759-1.05550.1670.7441-0.22630.08210.729-0.16480.656928.553217.81744.593
54.2959-0.1147-0.40682.6782-0.14964.9043-0.10940.5628-0.028-0.307-0.0487-0.20430.33980.00030.11410.6029-0.08520.06250.4242-0.10470.377248.160122.592134.4906
62.63251.41850.51964.26270.06063.81310.1153-0.1256-0.01240.4937-0.1060.0525-0.1703-0.02730.00010.40560.0009-0.01250.4580.11620.377154.146748.1274121.2825
74.22710.64960.70186.3106-1.96624.2635-0.11020.23110.09160.07570.29040.4342-0.1216-0.1128-0.18580.3281-0.0283-0.00540.55990.01970.469944.902940.8138105.8645
85.0545-0.13020.87741.51610.17153.59150.1003-0.3199-0.090.1969-0.21740.9310.4435-0.57530.11090.4334-0.11210.03090.6551-0.04540.771727.5131.3959109.5727
95.0043-0.55292.30462.97820.34851.2721-0.34660.7322-0.13210.2629-0.18340.7346-0.5393-1.35460.23890.6442-0.0296-0.1331.1592-0.14151.050620.273138.285598.383
105.035-2.0511.2766.1102-0.93093.46330.02630.8839-0.2724-0.8662-0.08320.18070.4223-0.18550.01590.5938-0.0943-0.09380.7577-0.08090.534636.446232.463993.5498
111.4341-1.2134-0.57984.8685-0.46682.5943-0.0253-0.33450.08580.2223-0.2115-0.81350.19180.21570.26210.52810.0567-0.12240.6530.15270.661784.008449.9885112.3724
123.47080.0856-0.18815.1110.43843.90810.0406-0.26420.02910.1067-0.1265-0.5628-0.066-0.01040.07890.49440.0223-0.0260.38480.13890.480175.965966.3688104.8978
132.47730.8464-0.1993.76990.3434.231-0.00760.099-0.2035-0.49550.0220.12740.1368-0.4914-0.01480.62940.05140.04240.40220.15260.420360.614566.015990.8745
141.863-0.89311.42135.1999-0.2532.0736-0.10010.0162-0.0073-0.2006-0.0212-0.3162-0.26030.05780.07610.68810.00780.14420.42670.11030.454969.694779.544696.6093
152.58680.8372-1.62323.27350.77784.89650.1990.24160.0292-0.3588-0.2960.1316-0.7318-0.79910.10310.50950.1315-0.06720.7829-0.19280.471438.2175105.544698.6305
161.94290.6935-0.04542.10530.21391.1127-0.01550.387-0.19370.1663-0.33630.51370.1885-1.29590.24930.6525-0.19260.09241.7005-0.58140.914418.354484.766798.1926
172.8393-0.56250.03593.6979-0.35863.8586-0.1541-0.16380.02520.07920.05110.1354-0.0416-0.04770.09150.50640.0994-0.03710.5671-0.01360.484767.687923.657386.0481
183.21010.67042.13926.06810.76614.4238-0.1955-0.2574-0.09640.30670.0199-0.0120.42740.17450.17960.60950.17680.11430.56030.05080.482276.43325.978788.9577
190.8695-0.0895-0.33863.24350.86551.7049-0.03410.0489-0.11990.04530.0905-0.48710.62710.6599-0.06230.84160.36520.06540.7390.05690.746791.1908-2.677383.2241
202.5341.3462-0.71164.8319-1.17173.51910.03260.167-0.2795-0.00070.4022-0.14951.10190.4807-0.44680.93150.0903-0.32250.6884-0.22891.0053-10.557335.8071109.4674
210.31160.2661-0.54870.6108-1.14812.25770.2298-0.05520.0993-0.12790.3748-0.1554-0.11221.1959-0.54080.6935-0.0603-0.12381.2688-0.55331.16359.356155.5683103.7444
223.5922.2805-1.27396.05790.49694.2343-0.74420.0188-0.6641-0.21090.64020.5081.0533-0.19710.35090.92390.10970.17910.5816-0.07411.20870.89029.064851.4055
232.82061.1453-1.60125.83920.04354.3967-0.49650.258-0.2101-0.02660.42911.220.431-0.69690.00930.577-0.1042-0.04370.58020.07791.2711-3.170521.679248.736
243.2177-1.4638-0.57876.98031.65553.8593-0.3809-0.02170.0375-0.49480.75170.7751-0.00240.3077-0.33440.5516-0.1579-0.07210.49180.03810.634311.494833.285443.4871
252.26360.07890.30395.25410.00982.3754-0.1564-0.03380.2342-0.79660.7138-0.4649-0.36740.6928-0.52570.7815-0.21620.10140.7694-0.32230.889723.878244.188443.9161
261.2784-1.3096-1.41235.17181.27581.7450.0827-0.13470.08620.5934-0.1023-0.85950.14980.10120.04260.5590.1369-0.10730.71760.22180.79193.099826.7291105.5739
274.4264-2.184-2.21612.20911.98224.03860.38210.7020.4814-0.4617-0.0936-0.8608-0.3331-0.3947-0.25780.63880.1830.09970.8310.29081.087198.895631.44192.8177
283.622-0.2864-1.05751.692-0.19081.77380.44350.51570.8091-0.3280.2285-0.5529-0.5537-0.064-0.64390.82810.22840.33210.9790.20681.3439116.452133.763382.6022
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 135 through 239 )A135 - 239
2X-RAY DIFFRACTION2chain 'A' and (resid 240 through 320 )A240 - 320
3X-RAY DIFFRACTION3chain 'A' and (resid 322 through 398 )A322 - 398
4X-RAY DIFFRACTION4chain 'A' and (resid 399 through 427 )A399 - 427
5X-RAY DIFFRACTION5chain 'A' and (resid 428 through 480 )A428 - 480
6X-RAY DIFFRACTION6chain 'B' and (resid 135 through 239 )B135 - 239
7X-RAY DIFFRACTION7chain 'B' and (resid 240 through 320 )B240 - 320
8X-RAY DIFFRACTION8chain 'B' and (resid 322 through 405 )B322 - 405
9X-RAY DIFFRACTION9chain 'B' and (resid 406 through 436 )B406 - 436
10X-RAY DIFFRACTION10chain 'B' and (resid 437 through 480 )B437 - 480
11X-RAY DIFFRACTION11chain 'C' and (resid 134 through 239 )C134 - 239
12X-RAY DIFFRACTION12chain 'C' and (resid 240 through 320 )C240 - 320
13X-RAY DIFFRACTION13chain 'C' and (resid 322 through 436 )C322 - 436
14X-RAY DIFFRACTION14chain 'C' and (resid 437 through 480 )C437 - 480
15X-RAY DIFFRACTION15chain 'D' and (resid 135 through 239 )D135 - 239
16X-RAY DIFFRACTION16chain 'D' and (resid 240 through 480 )D240 - 480
17X-RAY DIFFRACTION17chain 'E' and (resid 135 through 239 )E135 - 239
18X-RAY DIFFRACTION18chain 'E' and (resid 240 through 320 )E240 - 320
19X-RAY DIFFRACTION19chain 'E' and (resid 322 through 480 )E322 - 480
20X-RAY DIFFRACTION20chain 'F' and (resid 135 through 238 )F135 - 238
21X-RAY DIFFRACTION21chain 'F' and (resid 239 through 480 )F239 - 480
22X-RAY DIFFRACTION22chain 'G' and (resid 137 through 170 )G137 - 170
23X-RAY DIFFRACTION23chain 'G' and (resid 171 through 239 )G171 - 239
24X-RAY DIFFRACTION24chain 'G' and (resid 240 through 356 )G240 - 356
25X-RAY DIFFRACTION25chain 'G' and (resid 357 through 480 )G357 - 480
26X-RAY DIFFRACTION26chain 'H' and (resid 135 through 193 )H135 - 193
27X-RAY DIFFRACTION27chain 'H' and (resid 194 through 258 )H194 - 258
28X-RAY DIFFRACTION28chain 'H' and (resid 259 through 480 )H259 - 480

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  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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