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- PDB-6vzh: Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311 -

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Basic information

Entry
Database: PDB / ID: 6vzh
TitleStructure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311
ComponentsSerine/threonine-protein kinase VRK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC / TRANSFERASE-TRANSFERASE INHIBITOR / 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
Chem-RYA / Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
Authorsdos Reis, C.V. / Dutra, L.A. / Gama, F. / Ferreira, M. / Mascarello, A. / Azevedo, H. / Guimaraes, C. / Massirer, K.B. / Arruda, P. / Edwards, A.M. ...dos Reis, C.V. / Dutra, L.A. / Gama, F. / Ferreira, M. / Mascarello, A. / Azevedo, H. / Guimaraes, C. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Counago, R.M. / Structural Genomics Consortium (SGC)
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/50724-5 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)465651/2014-3 Brazil
Sao Paulo Research Foundation (FAPESP)2014/50897-0 Brazil
CitationJournal: To be Published
Title: Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311
Authors: dos Reis, C.V. / Dutra, L.A. / Gama, F. / Ferreira, M. / Mascarello, A. / Azevedo, H. / Guimaraes, C.R.W. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Counago, R.M.
History
DepositionFeb 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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)166,19816
Polymers164,5534
Non-polymers1,64512
Water57632
1
A: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3303
Polymers41,1381
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7865
Polymers41,1381
Non-polymers6484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3303
Polymers41,1381
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7525
Polymers41,1381
Non-polymers6144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.158, 95.641, 192.593
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 41138.125 Da / Num. of mol.: 4
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): R3
References: UniProt: Q99986, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-RYA / (7~{R})-2-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]amino]-5,7-dimethyl-8-prop-2-ynyl-7~{H}-pteridin-6-one


Mass: 359.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H15F2N5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 27.5% PEG3350, 300 mM lithium sulfate, 0.1 M sodium tartrate, 0.1 M Bis-Tris, 0.1 M glycylglycine, cryoprotectant: 30% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 5, 2019
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.55→96.3 Å / Num. obs: 56320 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.055 / Rrim(I) all: 0.142 / Net I/σ(I): 8.7 / Num. measured all: 376419 / Scaling rejects: 6
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
2.55-2.626.91.5593156545690.6760.6371.6861.199.9
10.82-96.35.90.04750328580.9980.0210.05225.599.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6BRU

6bru


Resolution: 2.55→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 30.444 / SU ML: 0.28 / SU R Cruickshank DPI: 0.4584 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.457 / ESU R Free: 0.278
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 2757 4.9 %RANDOM
Rwork0.2157 ---
obs0.2174 53338 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 143.64 Å2 / Biso mean: 63.234 Å2 / Biso min: 43.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2--2.27 Å2-0 Å2
3----1.73 Å2
Refinement stepCycle: final / Resolution: 2.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9562 0 101 32 9695
Biso mean--97.49 58.71 -
Num. residues----1244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0139886
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178843
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.64113461
X-RAY DIFFRACTIONr_angle_other_deg1.251.57720336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86551232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.07921.883494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.016151492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9561559
X-RAY DIFFRACTIONr_chiral_restr0.0650.21275
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022126
LS refinement shellResolution: 2.55→2.615 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 231 -
Rwork0.35 3804 -
all-4035 -
obs--99.9 %
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)
11.4902-0.5493-1.44831.67591.22533.28590.03960.07740.11660.1294-0.0532-0.077-0.0998-0.11710.01350.3611-0.0114-0.00220.35480.00550.023218.45342.439220.9211
22.7455-0.20990.31212.2253-0.39021.8604-0.0390.0319-0.1376-0.01370.08120.3913-0.031-0.418-0.04220.46540.00970.02390.4573-0.00860.0751-15.13082.497552.7564
31.1593-0.00630.92211.7739-0.67553.60430.0163-0.0365-0.06380.1524-0.05050.2320.2128-0.37090.03420.2943-0.08280.03940.4279-0.03730.0453-25.8355-45.007727.7049
42.6237-0.5114-0.82452.37040.80742.9654-0.0143-0.12470.53060.12460.1489-0.2452-0.13010.1107-0.13460.29740.0047-0.03580.4287-0.01970.1201-26.689-9.798-2.6565
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 402
2X-RAY DIFFRACTION2B23 - 501
3X-RAY DIFFRACTION3C21 - 402
4X-RAY DIFFRACTION4D22 - 501

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