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- PDB-6ac9: Crystal structure of human Vaccinia-related kinase 1 (VRK1) in co... -

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Basic information

Entry
Database: PDB / ID: 6ac9
TitleCrystal structure of human Vaccinia-related kinase 1 (VRK1) in complex with AMP-PNP
ComponentsSerine/threonine-protein kinase VRK1
KeywordsTRANSFERASE / Kinase / Vaccinia-related kinase / VRK1 / Adenosine triphosphate / ATP / AMP-PNP
Function / homology
Function and homology information


histone H2AX kinase activity / Cajal body organization / Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / regulation of neuron migration / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation ...histone H2AX kinase activity / Cajal body organization / Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / regulation of neuron migration / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / histone H3S10 kinase activity / Cajal body / nucleosomal DNA binding / neuron projection development / kinase activity / histone binding / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / protein phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / chromatin / 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. ...: / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsNgow, Y.S. / Sreekanth, R. / Yoon, H.S.
CitationJournal: Protein Sci. / Year: 2019
Title: Crystal structure of human vaccinia-related kinase 1 in complex with AMP-PNP, a non-hydrolyzable ATP analog.
Authors: Ngow, Y.S. / Rajan, S. / Ye, H. / Yoon, H.S.
History
DepositionJul 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)171,41727
Polymers167,9084
Non-polymers3,50923
Water16,015889
1
A: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9297
Polymers41,9771
Non-polymers9526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15020 Å2
MethodPISA
2
B: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0258
Polymers41,9771
Non-polymers1,0487
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14700 Å2
MethodPISA
3
C: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7316
Polymers41,9771
Non-polymers7545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14420 Å2
MethodPISA
4
D: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7316
Polymers41,9771
Non-polymers7545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-11 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.596, 96.846, 192.520
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: 41977.031 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): BL21(DE3)
References: UniProt: Q99986, non-specific serine/threonine protein kinase

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Non-polymers , 7 types, 912 molecules

#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 889 / 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: 2.57 Å3/Da / Density % sol: 52.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 27.5 % w/v PEG 3350, 0.2 M of ammonium sulfate, 0.1 M of HEPES (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.07→68 Å / Num. obs: 106113 / % possible obs: 100 % / Redundancy: 22.4 % / Biso Wilson estimate: 32.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Net I/σ(I): 21.3
Reflection shellResolution: 2.07→2.11 Å / Redundancy: 22.5 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 5210 / CC1/2: 0.968 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
iMOSFLMdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.223 5014 4.76 %RANDOM
Rwork0.186 ---
obs0.187 105361 99.5 %-
Displacement parametersBiso mean: 41.22 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: 1 / Resolution: 2.07→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9946 0 205 889 11040
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3654SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes246
X-RAY DIFFRACTIONt_gen_planes1538HARMONIC5
X-RAY DIFFRACTIONt_it10418HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1297SEMIHARMONIC5
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_contact12746SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10418HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg14113HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion16.74
LS refinement shellResolution: 2.07→2.12 Å
RfactorNum. reflection% reflection
Rfree0.259 377 4.89 %
Rwork0.223 7335 -
obs--99.99 %

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