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- PDB-5vd9: Crystal structure of human WEE1 kinase domain in complex with RAC... -

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Basic information

Entry
Database: PDB / ID: 5vd9
TitleCrystal structure of human WEE1 kinase domain in complex with RAC-IV-097, a MK1775 analogue
ComponentsWee1-like protein kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / KINASE DOMAIN / CELL CYCLE / WEE1 / TRANSFERASE / INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


G2/M DNA replication checkpoint / negative regulation of G2/M transition of mitotic cell cycle / Polo-like kinase mediated events / negative regulation of G1/S transition of mitotic cell cycle / establishment of cell polarity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / neuron projection morphogenesis ...G2/M DNA replication checkpoint / negative regulation of G2/M transition of mitotic cell cycle / Polo-like kinase mediated events / negative regulation of G1/S transition of mitotic cell cycle / establishment of cell polarity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / neuron projection morphogenesis / positive regulation of DNA replication / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / microtubule cytoskeleton organization / G2/M transition of mitotic cell cycle / Factors involved in megakaryocyte development and platelet production / protein tyrosine kinase activity / cell division / nucleolus / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Wee1-like protein kinase / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 ...Wee1-like protein kinase / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-98G / Wee1-like protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å
AuthorsZhu, J.-Y. / Schonbrunn, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)UO1 HD076542 United States
CitationJournal: to be published
Title: Structural basis of Wee family kinase inhibition by small molecules
Authors: Zhu, J.-Y. / Schonbrunn, E.
History
DepositionApr 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: Wee1-like protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0254
Polymers32,4411
Non-polymers5843
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.370, 44.590, 64.590
Angle α, β, γ (deg.)90.000, 102.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Wee1-like protein kinase / WEE1hu / Wee1A kinase


Mass: 32440.900 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 291-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WEE1 / Plasmid: pET28a / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-RIPL
References: UniProt: P30291, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-98G / 1-{6-[(1R)-1-hydroxyethyl]pyridin-2-yl}-6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one


Mass: 486.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H30N8O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 5.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 7.5 % PEG 3350, 1 mM RAC-IV-097

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 8, 2016
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→33.053 Å / Num. obs: 23118 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.678 % / Biso Wilson estimate: 29.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.052 / Χ2: 0.996 / Net I/σ(I): 17.77
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.87-1.923.6040.284.7916860.9490.32998.8
1.92-1.973.6240.2226.116430.9620.26198.1
1.97-2.033.5990.1737.5515940.9740.20497.9
2.03-2.093.5960.1458.9715900.9840.1799.5
2.09-2.163.6020.11310.7714860.9870.13398.5
2.16-2.243.6950.09712.6614760.9920.11498.3
2.24-2.323.7530.08314.4614310.9940.09799.7
2.32-2.413.7660.0716.5413520.9940.08298.9
2.41-2.523.7580.06218.3713260.9950.07398.5
2.52-2.643.7580.05719.912490.9950.06799
2.64-2.793.7340.0522.0612200.9960.05899
2.79-2.963.7380.04624.7711210.9970.05498.8
2.96-3.163.7310.04127.4610710.9960.04898.8
3.16-3.413.7230.03929.699890.9960.04698.5
3.41-3.743.7090.03631.569230.9970.04299.4
3.74-4.183.6880.03732.278210.9960.04498.9
4.18-4.833.7070.03433.237400.9970.0498.5
4.83-5.913.6230.03432.66280.9970.03999.1
5.91-8.363.6160.03233.15030.9970.03898.4
8.36-33.0533.2570.0432.242690.9960.04994.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SERGUIdata collection
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V5Y

5v5y


Resolution: 1.87→33.053 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.82
RfactorNum. reflection% reflection
Rfree0.2529 1156 5 %
Rwork0.2016 --
obs-23118 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 220.83 Å2 / Biso mean: 55.3207 Å2 / Biso min: 16.88 Å2
Refinement stepCycle: final / Resolution: 1.87→33.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 77 62 2218
Biso mean--43.22 38.43 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142166
X-RAY DIFFRACTIONf_angle_d1.4622922
X-RAY DIFFRACTIONf_chiral_restr0.059314
X-RAY DIFFRACTIONf_plane_restr0.008373
X-RAY DIFFRACTIONf_dihedral_angle_d18.927816
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8699-1.9550.30241410.24282685282698
1.955-2.0580.29881430.22812717286099
2.058-2.1870.271450.21692752289799
2.187-2.35580.24931420.21932711285399
2.3558-2.59280.29031460.22132762290899
2.5928-2.96770.25121450.2282757290299
2.9677-3.73820.25441450.20122765291099
3.7382-33.05830.23251490.17122813296299
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)
15.5189-2.2794-0.99233.84911.69542.4967-0.12280.2965-0.4852-0.33050.14430.29080.4061-0.1953-0.0920.2977-0.0197-0.00990.27290.06920.2758-10.0716-4.13638.2099
23.2856-0.10251.56963.053-0.86253.2604-0.1299-0.31880.07820.24820.0917-0.0989-0.2022-0.1519-0.06840.2080.02480.0350.18570.03740.14131.3044.487317.6147
32.59392.10080.28312.2331-1.25974.180.31970.9742-0.2677-0.4662-0.3845-0.68370.68180.66780.39170.25070.07960.05920.3980.11690.413413.6004-0.674513.4977
43.3898-0.60740.51413.1662-0.52651.5097-0.31380.03191.05190.4576-0.2551-1.3165-0.41190.4517-0.62530.4115-0.0591-0.17370.37610.09610.673417.988413.850318.774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 292 through 337 )A292 - 337
2X-RAY DIFFRACTION2chain 'A' and (resid 338 through 461 )A338 - 461
3X-RAY DIFFRACTION3chain 'A' and (resid 462 through 484 )A462 - 484
4X-RAY DIFFRACTION4chain 'A' and (resid 485 through 571 )A485 - 571

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