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- PDB-6bu6: Crystal Structure of the Human vaccinia-related kinase bound to a... -

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Basic information

Entry
Database: PDB / ID: 6bu6
TitleCrystal Structure of the Human vaccinia-related kinase bound to a bis-difluorophenol-aminopyridine 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


histone H2AX kinase activity / Golgi disassembly / Cajal body organization / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / regulation of neuron migration / nucleosomal DNA binding ...histone H2AX kinase activity / Golgi disassembly / Cajal body organization / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / regulation of neuron migration / nucleosomal DNA binding / Cajal body / neuron projection development / kinase activity / histone H3T3 kinase activity / histone H3S10 kinase activity / protein autophosphorylation / histone binding / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / 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 / cytosol / cytoplasm
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-E8V / Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCounago, R.M. / dos Reis, C.V. / de Souza, G.P. / Santiago, A.S. / Azevedo, A. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Massirer, K.B. ...Counago, R.M. / dos Reis, C.V. / de Souza, G.P. / Santiago, A.S. / 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 bis-difluorophenol-aminopyridine inhibitor
Authors: Counago, R.M. / dos Reis, C.V. / de Souza, G.P. / Santiago, A.S. / Azevedo, H. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / ...Authors: Counago, R.M. / dos Reis, C.V. / de Souza, G.P. / Santiago, A.S. / 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
DepositionDec 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)166,38819
Polymers164,5534
Non-polymers1,83615
Water21,0601169
1
A: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6515
Polymers41,1381
Non-polymers5134
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)41,6555
Polymers41,1381
Non-polymers5174
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)41,3664
Polymers41,1381
Non-polymers2283
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)41,7165
Polymers41,1381
Non-polymers5784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.215, 96.572, 193.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEAA23 - 34123 - 341
21PHEPHEBB23 - 34123 - 341
12GLUGLUAA21 - 34121 - 341
22GLUGLUCC21 - 34121 - 341
13GLNGLNAA22 - 34122 - 341
23GLNGLNDD22 - 34122 - 341
14PHEPHEBB23 - 34123 - 341
24PHEPHECC23 - 34123 - 341
15PHEPHEBB23 - 34123 - 341
25PHEPHEDD23 - 34123 - 341
16GLNGLNCC22 - 34122 - 341
26GLNGLNDD22 - 34122 - 341

NCS ensembles :
ID
1
2
3
4
5
6

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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 / Details (production host): pNIC28-Bsa4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99986, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 1184 molecules

#2: Chemical ChemComp-E8V / 4,4'-(2-aminopyridine-3,5-diyl)bis(2,6-difluorophenol)


Mass: 350.267 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H10F4N2O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1169 / 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: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 22% PEG3350; 0.02M Lithium Sulfate; 0.1M Buffer system SBG pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→19.98 Å / Num. obs: 159713 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.052 / Rrim(I) all: 0.139 / Net I/σ(I): 13.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 13.6 % / Rmerge(I) obs: 2.177 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7810 / CC1/2: 0.698 / Rpim(I) all: 0.882 / Rrim(I) all: 2.349 / % 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: 1.8→19.98 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.994 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 8093 5.1 %RANDOM
Rwork0.18403 ---
obs0.18551 151521 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.218 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--2.34 Å2-0 Å2
3----2.16 Å2
Refinement stepCycle: 1 / Resolution: 1.8→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9904 0 112 1173 11189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01910334
X-RAY DIFFRACTIONr_bond_other_d0.0020.029375
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.96714027
X-RAY DIFFRACTIONr_angle_other_deg0.9682.99821686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84351275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.67723.582469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92151699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4331568
X-RAY DIFFRACTIONr_chiral_restr0.0920.21486
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111570
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022167
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_it2.3843.2975073
X-RAY DIFFRACTIONr_mcbond_other2.3823.2965072
X-RAY DIFFRACTIONr_mcangle_it3.4864.9256336
X-RAY DIFFRACTIONr_mcangle_other3.4874.9256337
X-RAY DIFFRACTIONr_scbond_it2.8593.4125261
X-RAY DIFFRACTIONr_scbond_other2.8593.4125261
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3725.0397685
X-RAY DIFFRACTIONr_long_range_B_refined6.31538.38312319
X-RAY DIFFRACTIONr_long_range_B_other6.15537.74412013
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A196780.1
12B196780.1
21A213480.07
22C213480.07
31A203000.1
32D203000.1
41B192640.1
42C192640.1
51B200680.07
52D200680.07
61C199820.09
62D199820.09
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 627 -
Rwork0.302 11054 -
obs--100 %

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