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- PDB-6cmm: Crystal Structure of the Human vaccinia-related kinase bound to a... -

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Basic information

Entry
Database: PDB / ID: 6cmm
TitleCrystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine inhibitor
ComponentsSerine/threonine-protein kinase VRK1
KeywordsTransferase/Transferase Inhibitor / transferase / protein kinase domain / Structural Genomics / Structural Genomics Consortium / SGC / Transferase-Transferase Inhibitor Complex
Function / homology
Function and homology information


Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / histone H3S10 kinase activity / kinase activity / histone binding ...Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / histone H3S10 kinase activity / kinase activity / histone binding / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / nucleolus / protein kinase binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 ...Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Chem-F7D / DI(HYDROXYETHYL)ETHER / Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
Authorsdos Reis, C.V. / de Souza, G.P. / Counago, R.M. / Azevedo, A. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Massirer, K.B. / Arruda, P. ...dos Reis, C.V. / de Souza, G.P. / Counago, R.M. / Azevedo, A. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Elkins, J.M. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/50724-5 Brazil
CitationJournal: To Be Published
Title: Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine inhibitor
Authors: dos Reis, C.V. / de Souza, G.P. / Counago, R.M. / Azevedo, H. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Elkins, J.M. / ...Authors: dos Reis, C.V. / de Souza, G.P. / Counago, R.M. / Azevedo, H. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Elkins, J.M. / Structural Genomics Consortium (SGC)
History
DepositionMar 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase VRK1
B: Serine/threonine-protein kinase VRK1
C: Serine/threonine-protein kinase VRK1
D: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,47421
Polymers164,5534
Non-polymers1,92217
Water8,539474
1
A: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2563
Polymers41,1381
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9978
Polymers41,1381
Non-polymers8597
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3524
Polymers41,1381
Non-polymers2143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8696
Polymers41,1381
Non-polymers7315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.058, 95.753, 192.833
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Serine/threonine-protein kinase VRK1 / Vaccinia-related kinase 1


Mass: 41138.125 Da / Num. of mol.: 4 / Fragment: residues 3-364
Mutation: K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VRK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): R3
References: UniProt: Q99986, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 491 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C2H3O2
#3: Chemical ChemComp-F7D / (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one


Mass: 383.352 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H15F2N5O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30.25% PEG3350, 200 mM LiSO4, 0.1M SBG buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.1→29.79 Å / Num. obs: 100045 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.075 / Rrim(I) all: 0.142 / Net I/σ(I): 10.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.118 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.691 / Rpim(I) all: 0.711 / Rrim(I) all: 1.344 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OP5

3op5


Resolution: 2.1→29.79 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 10.939 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.158 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22201 5052 5.1 %RANDOM
Rwork0.19029 ---
obs0.19191 94907 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.019 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2--0.32 Å2-0 Å2
3----1.03 Å2
Refinement stepCycle: 1 / Resolution: 2.1→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9901 0 125 474 10500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01910342
X-RAY DIFFRACTIONr_bond_other_d0.0020.029422
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9714026
X-RAY DIFFRACTIONr_angle_other_deg0.9672.99621761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16951267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.82223.473478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.634151692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9411572
X-RAY DIFFRACTIONr_chiral_restr0.0830.21497
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111569
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022163
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5621.5385064
X-RAY DIFFRACTIONr_mcbond_other0.5471.5315055
X-RAY DIFFRACTIONr_mcangle_it0.9542.296312
X-RAY DIFFRACTIONr_mcangle_other0.9542.2916313
X-RAY DIFFRACTIONr_scbond_it0.7151.6275278
X-RAY DIFFRACTIONr_scbond_other0.7151.6275279
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0632.4197710
X-RAY DIFFRACTIONr_long_range_B_refined4.49718.21511653
X-RAY DIFFRACTIONr_long_range_B_other4.49718.2211654
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 357 -
Rwork0.278 6930 -
obs--99.99 %
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)
14.42630.87920.19686.48221.86525.38310.0883-0.04660.36350.18420.0986-0.4643-0.28630.088-0.18690.10320.03190.04040.32020.00370.102334.772-1.36063.8754
20.9604-0.7861-0.78442.87071.34712.05390.10690.16730.0422-0.1788-0.1274-0.0099-0.1855-0.15670.02050.17080.02030.02270.391-0.00670.007619.17460.775815.2427
30.0948-0.21330.45890.6257-1.26322.61870.06680.1278-0.03790.0681-0.2982-0.2143-0.03890.5570.23140.7403-0.0807-0.18330.4679-0.02670.932916.0745-12.80130.6275
40.88790.3392-0.82382.9786-0.16783.5752-0.0005-0.03830.13320.34940.0018-0.1045-0.01540.0445-0.00130.22460.01790.00350.3038-0.04250.042615.85895.00136.9944
50.4206-0.0026-0.38086.8327-0.82032.59490.08520.00540.1899-0.134-0.26750.5223-0.2648-0.35220.18220.19240.08990.01340.4563-0.09740.21114.944910.362626.4219
67.6014.9015-4.133811.0957-2.98164.13510.09590.17630.30.2577-0.09841.0062-0.3508-0.4520.00250.34390.0251-0.14810.4780.07920.544-35.700916.409543.4345
78.99881.03022.57923.6866-0.07365.6828-0.0142-0.0557-0.1387-0.38240.06310.8155-0.1244-0.7406-0.04890.3092-0.0221-0.04070.47390.00720.5231-38.06210.225542.2843
84.9811-0.1832-0.77344.2756-0.05092.1849-0.09750.20370.4422-0.23480.25770.2719-0.3189-0.1525-0.16010.2435-0.0055-0.06860.3710.01750.1117-19.051210.769142.9426
91.63140.2779-0.10162.9171-0.9482.0960.01040.0529-0.0496-0.08230.0470.49330.0952-0.341-0.05750.1679-0.045-0.00730.377-0.01710.0952-19.03161.894950.0809
101.84010.5678-0.16482.4403-0.13612.5291-0.045-0.1628-0.22630.0085-0.02320.04780.2552-0.03220.06820.1648-0.00630.00720.32210.0270.0353-7.4206-2.489560.5992
115.4481.60762.46686.09872.112.9455-0.1170.1421-0.6883-0.00380.1780.24090.3999-0.1541-0.0610.4767-0.04930.03380.35870.04840.1591-19.1171-62.007546.427
123.4921-0.37990.89662.6765-0.63933.2528-0.0234-0.2101-0.09390.25870.00130.12030.3237-0.23680.02210.1807-0.07030.01110.33560.01880.0103-18.7196-47.780739.1696
132.5866-0.3711.1151.552-0.66692.4349-0.0212-0.1421-0.23810.1920.01140.18340.3243-0.36870.00980.1233-0.0920.05480.4413-0.0190.0523-26.8841-46.555830.257
145.0005-2.1802-0.71130.96780.31040.1877-0.20320.056-0.50740.11870.04690.15810.22710.01920.15630.58920.0174-0.00880.65720.00370.5354-11.0143-43.613916.7967
153.02250.03440.09371.2840.22572.6382-0.11510.05210.0685-0.0194-0.0810.268-0.0367-0.44860.19610.0513-0.0069-0.02340.4308-0.01210.0723-31.5609-38.86716.3237
167.3252.9391.16612.71591.33110.6888-0.030.39981.0896-0.2160.1214-0.03-0.2044-0.0069-0.09140.46890.10080.1310.5301-0.11930.5604-40.515111.02347.8084
176.96022.46412.00015.30311.43914.6223-0.10410.26410.6588-0.23240.19090.0619-0.86460.2367-0.08690.35270.05710.06130.382-0.05730.4508-34.1958.59084.6475
181.956-0.0347-0.63381.44990.63932.61150.0203-0.14720.3160.10660.0944-0.0281-0.1638-0.0035-0.11470.03620.0091-0.00590.3428-0.01830.0584-28.6355-10.0584-1.3469
196.2274-2.75251.82443.9177-1.32593.90110.00610.39110.0004-0.2798-0.0653-0.29570.1030.2910.05920.0741-0.02890.05820.3705-0.02230.0765-16.6563-16.5806-19.8026
204.86740.58890.4451.11370.46392.5742-0.1169-0.35290.02570.08260.105-0.31640.13870.31860.0120.10060.0979-0.03550.3911-0.0260.108-17.0229-22.3219-1.7866
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 71
2X-RAY DIFFRACTION2A72 - 209
3X-RAY DIFFRACTION3A210 - 222
4X-RAY DIFFRACTION4A223 - 290
5X-RAY DIFFRACTION5A291 - 341
6X-RAY DIFFRACTION6B23 - 43
7X-RAY DIFFRACTION7B50 - 63
8X-RAY DIFFRACTION8B64 - 114
9X-RAY DIFFRACTION9B115 - 206
10X-RAY DIFFRACTION10B207 - 341
11X-RAY DIFFRACTION11C21 - 61
12X-RAY DIFFRACTION12C62 - 121
13X-RAY DIFFRACTION13C122 - 210
14X-RAY DIFFRACTION14C211 - 222
15X-RAY DIFFRACTION15C223 - 341
16X-RAY DIFFRACTION16D22 - 41
17X-RAY DIFFRACTION17D42 - 77
18X-RAY DIFFRACTION18D78 - 260
19X-RAY DIFFRACTION19D261 - 294
20X-RAY DIFFRACTION20D295 - 341

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