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- PDB-5uvf: Crystal Structure of the Human vaccinia-related kinase bound to B... -

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Basic information

Entry
Database: PDB / ID: 5uvf
TitleCrystal Structure of the Human vaccinia-related kinase bound to BI-D1870
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


histone H2AX kinase activity / Golgi disassembly / Cajal body organization / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / histone H3S10 kinase activity / regulation of neuron migration / Initiation of Nuclear Envelope (NE) Reformation ...histone H2AX kinase activity / Golgi disassembly / Cajal body organization / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / histone H3S10 kinase activity / regulation of neuron migration / Initiation of Nuclear Envelope (NE) Reformation / Golgi stack / nucleosomal DNA binding / Cajal body / neuron projection development / kinase activity / protein autophosphorylation / histone binding / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / cell division / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / protein kinase binding / chromatin / nucleolus / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / 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. ...: / 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
Chem-7DZ / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCounago, R.M. / Bountra, C. / Arruda, P. / Edwards, A.M. / Gileadi, O. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/50724-5 Brazil
CitationJournal: Sci Rep / Year: 2017
Title: Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations.
Authors: Counago, R.M. / Allerston, C.K. / Savitsky, P. / Azevedo, H. / Godoi, P.H. / Wells, C.I. / Mascarello, A. / de Souza Gama, F.H. / Massirer, K.B. / Zuercher, W.J. / Guimaraes, C.R.W. / Gileadi, O.
History
DepositionFeb 20, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionMar 22, 2017ID: 5UGE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Author supporting evidence / Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.grant_number
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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)167,20920
Polymers164,5534
Non-polymers2,65716
Water12,304683
1
A: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7194
Polymers41,1381
Non-polymers5813
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)41,6253
Polymers41,1381
Non-polymers4862
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)42,0518
Polymers41,1381
Non-polymers9137
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)41,8145
Polymers41,1381
Non-polymers6764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.141, 95.242, 192.040
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: UNP RESIDUES 3-364 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VRK1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DE3 / Variant (production host): R3
References: UniProt: Q99986, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 699 molecules

#2: Chemical
ChemComp-7DZ / (7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8-dihydropteridin-6(5H)-one / BI-D1870


Mass: 391.415 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H23F2N5O2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 683 / 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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG3350, 0.1M BISTRIS, 0.2M, LITHIUM SULFATE, PH 6.5
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→29.66 Å / Num. obs: 156295 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 41.72 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.943 / Mean I/σ(I) obs: 0.5 / % possible all: 96.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OP5

3op5


Resolution: 2→29.66 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.139 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.126
RfactorNum. reflection% reflectionSelection details
Rfree0.204 5538 4.99 %RANDOM
Rwork0.173 ---
obs0.175 110975 96.8 %-
Displacement parametersBiso mean: 52.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.6299 Å20 Å20 Å2
2---12.1543 Å20 Å2
3---10.5244 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9597 0 170 683 10450
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019995HARMONIC2
X-RAY DIFFRACTIONt_angle_deg113574HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3430SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes221HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1458HARMONIC5
X-RAY DIFFRACTIONt_it9995HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion16.23
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1264SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12016SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 381 4.6 %
Rwork0.204 7901 -
all0.205 8282 -
obs--98.94 %
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)
13.158-1.28570.24654.63982.71626.35310.0974-0.13440.22320.04670.3247-0.7003-0.29260.5357-0.4221-0.0809-0.05390.08290.1185-0.0499-0.088535.3881-3.28793.7792
24.94320.5311-0.091.60954.50633.6799-0.01910.52290.2841-0.44140.352-0.5437-0.78160.2374-0.3329-0.0728-0.07470.12060.007-0.0976-0.118833.5522-1.54145.6345
35.1095-2.83710.64476.38931.51790.41560.12190.3557-0.1693-0.8573-0.2460.3136-0.3908-0.29910.12420.13280.10510.0150.0649-0.0355-0.208315.539-5.556710.5673
40.717-0.4679-0.73982.12271.61342.25660.14450.14130.1451-0.1947-0.1209-0.196-0.4036-0.0757-0.02360.03690.01990.03430.0116-0.0167-0.109920.07923.308116.2202
51.49130.49810.05872.95141.18593.539-0.02110.026-0.10530.2388-0.083-0.13690.3707-0.13190.1041-0.00550.01370.0564-0.0448-0.0667-0.188714.7902-2.610530.6239
62.2224-0.1888-0.13142.2359-0.08662.8221-0.0564-0.12740.2350.350.0376-0.1331-0.29970.0750.01880.1255-0.0060.0188-0.0969-0.0631-0.154315.39759.073641.3309
71.5416-0.3922-0.05774.3067-0.07562.9983-0.0119-0.05180.2342-0.2347-0.30260.4111-0.3248-0.58160.3145-0.04410.1181-0.00050.0979-0.1648-0.11354.33439.519825.1525
82.56140.89741.17263.36212.69854.1286-0.10870.051-0.40730.15950.10070.16250.856-0.22270.00810.1615-0.10840.01-0.21770.0691-0.1714-18.1872-61.599645.2584
91.7222-1.06982.72814.8726-1.26174.7970.1685-0.187-0.49530.3469-0.07270.30010.8398-0.4557-0.09580.142-0.2055-0.0398-0.15040.0348-0.07-19.486-60.083642.4053
102.8553-0.33670.85822.59980.33042.859-0.0613-0.224-0.03920.2652-0.02150.0630.1109-0.08220.0828-0.013-0.0401-0.0142-0.05040.0325-0.1915-16.6961-42.927137.9149
113.55590.30592.26920.0134-0.57743.1346-0.0009-0.3033-0.21620.05990.04010.20420.3369-0.3554-0.0393-0.0005-0.05430.0571-0.08670.0315-0.1953-19.7708-47.564940.4678
121.6434-0.26550.66791.5918-0.62862.1028-0.0215-0.0694-0.388-0.02030.14220.19620.6329-0.5723-0.12070.1124-0.20140.01250.05160.0288-0.0488-27.9055-55.542531.7415
132.4387-0.23830.61521.149-0.26373.2867-0.0913-0.1398-0.07570.20580.05340.19980.1292-0.47410.0379-0.0277-0.0591-0.00280.03540.0066-0.1006-26.7952-42.856730.2054
145.84471.3009-1.011700.43222.5571-0.06980.2996-0.4546-0.0120.0377-0.40590.11560.5050.0321-0.051-0.0492-0.10350.18310.0402-0.058-10.1301-40.541219.2133
151.1352-0.10671.16150.38110.06913.14730.00560.1526-0.0425-0.04070.0350.13590.1496-0.2362-0.0407-0.0668-0.051-0.05290.0122-0.0011-0.1216-26.428-42.449816.8369
162.6899-0.5455-0.08661.5783-0.55852.0664-0.0270.3897-0.1065-0.207-0.00780.34040.1788-0.72140.0348-0.057-0.0787-0.09720.219-0.0237-0.0826-33.9545-42.75217.9944
175.6046-1.66571.13992.3163-0.6494.8056-0.06380.11990.2756-0.0487-0.06650.2041-0.2652-0.32630.1304-0.1115-0.0049-0.094-0.09020.0277-0.1292-27.4192-30.678217.9391
180.9353-1.0751-1.52671.2757-1.50144.31720.0425-0.39130.33690.14120.0870.5355-0.3627-0.8794-0.1295-0.12370.1012-0.0180.2329-0.0126-0.0589-38.8994-33.047629.3823
196.5108-1.2569-0.11776.01140.71421.7143-0.3040.26770.1788-0.19410.31450.971-0.0219-0.2497-0.0104-0.1075-0.0326-0.0987-0.16870.0922-0.0948-23.249111.187243.1146
202.10690.23350.10391.9025-0.37561.1905-0.04220.1294-0.0675-0.10080.06790.42760.0864-0.2342-0.0257-0.0391-0.0206-0.0124-0.1362-0.0032-0.0957-17.53883.703350.083
211.63510.1253-0.06990.9145-0.17171.8833-0.039-0.2388-0.3560.0594-0.00770.1080.2196-0.07970.04670.04110.00130.0171-0.1090.0451-0.0483-7.8547-4.108960.9279
223.9661-0.90932.41554.80550.87332.7425-0.0191-0.13970.55990.1262-0.0411-0.0504-0.4686-0.26610.06020.29210.29050.3555-0.2929-0.03620.176-36.47989.40977.9055
231.53230.7926-2.73872.2658-0.93920.2021-0.02190.25120.59570.06440.48570.5675-0.352-0.855-0.4639-0.1530.14330.06720.02810.1026-0.0409-39.4203-2.77130.9031
244.82390.96070.5184.1714-0.99227.340.2175-0.73990.0790.70740.0203-0.09210.059-0.0917-0.2379-0.0830.025-0.0115-0.0307-0.0422-0.1881-29.2303-14.034712.7794
252.55850.1998-1.87381.3204-0.76884.01840.2273-0.2310.52210.29140.0964-0.0181-0.64840.1936-0.3236-0.04040.00650.0354-0.0159-0.0792-0.0162-24.1562-6.05171.852
261.67690.13190.13081.11570.04792.6555-0.06020.13530.0655-0.0820.10590.0859-0.0347-0.2549-0.0458-0.12630.0215-0.00050.0690.0239-0.0736-30.3103-15.3695-10.2978
274.7781-0.73661.56042.2302-0.51983.9215-0.02950.47190.0088-0.3323-0.0447-0.19580.12490.38970.0742-0.1283-0.02510.07140.1218-0.0005-0.0824-15.7366-15.8285-19.308
282.75860.7673-0.61181.89170.10842.785-0.1184-0.492-0.08690.06810.0453-0.23740.27980.44220.0732-0.15120.1088-0.02970.1014-0.0388-0.0989-16.8415-22.5066-1.0489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|20 - 56}
2X-RAY DIFFRACTION2{A|57 - 77}
3X-RAY DIFFRACTION3{A|78 - 103}
4X-RAY DIFFRACTION4{A|104 - 205}
5X-RAY DIFFRACTION5{A|206 - 256}
6X-RAY DIFFRACTION6{A|257 - 296}
7X-RAY DIFFRACTION7{A|297 - 341}
8X-RAY DIFFRACTION8{B|22 - 56}
9X-RAY DIFFRACTION9{B|57 - 77}
10X-RAY DIFFRACTION10{B|78 - 102}
11X-RAY DIFFRACTION11{B|103 - 121}
12X-RAY DIFFRACTION12{B|122 - 150}
13X-RAY DIFFRACTION13{B|151 - 205}
14X-RAY DIFFRACTION14{B|206 - 223}
15X-RAY DIFFRACTION15{B|224 - 256}
16X-RAY DIFFRACTION16{B|257 - 296}
17X-RAY DIFFRACTION17{B|297 - 316}
18X-RAY DIFFRACTION18{B|317 - 341}
19X-RAY DIFFRACTION19{C|30 - 112}
20X-RAY DIFFRACTION20{C|113 - 216}
21X-RAY DIFFRACTION21{C|217 - 341}
22X-RAY DIFFRACTION22{D|26 - 67}
23X-RAY DIFFRACTION23{D|68 - 90}
24X-RAY DIFFRACTION24{D|91 - 112}
25X-RAY DIFFRACTION25{D|113 - 195}
26X-RAY DIFFRACTION26{D|196 - 256}
27X-RAY DIFFRACTION27{D|257 - 296}
28X-RAY DIFFRACTION28{D|297 - 341}

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