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- PDB-3i6u: Structure and Activation Mechanism of the CHK2 DNA-Damage Checkpo... -

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Basic information

Entry
Database: PDB / ID: 3i6u
TitleStructure and Activation Mechanism of the CHK2 DNA-Damage Checkpoint Kinase
ComponentsSerine/threonine-protein kinase Chk2
KeywordsTRANSFERASE / Ser/Thr protein kinase / FHA domain / ATP-binding / Cell cycle / Disease mutation / Kinase / Li-Fraumeni syndrome / Magnesium / Metal-binding / Nucleotide-binding / Nucleus / Phosphoprotein / Proto-oncogene / Serine/threonine-protein kinase
Function / homology
Function and homology information


mitotic DNA damage checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / thymocyte apoptotic process / regulation of protein catabolic process / replicative senescence / mitotic spindle assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex ...mitotic DNA damage checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / thymocyte apoptotic process / regulation of protein catabolic process / replicative senescence / mitotic spindle assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Stabilization of p53 / protein catabolic process / G2/M DNA damage checkpoint / Regulation of TP53 Activity through Methylation / cellular response to gamma radiation / PML body / G2/M transition of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to DNA damage / double-strand break repair / Regulation of TP53 Degradation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ubiquitin protein ligase binding / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase Chk2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPavletich, N.P.
CitationJournal: Mol.Cell / Year: 2009
Title: Structure and activation mechanism of the CHK2 DNA damage checkpoint kinase.
Authors: Cai, Z. / Chehab, N.H. / Pavletich, N.P.
History
DepositionJul 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Assembly

Deposited unit
A: Serine/threonine-protein kinase Chk2
B: Serine/threonine-protein kinase Chk2


Theoretical massNumber of molelcules
Total (without water)96,2262
Polymers96,2262
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-21 kcal/mol
Surface area37020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.900, 152.200, 52.400
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
22B
13A
23B

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRVALVALAA89 - 1506 - 67
211THRTHRVALVALBB89 - 1506 - 67
121TYRTYRLEULEUAA156 - 20473 - 121
221TYRTYRLEULEUBB156 - 20473 - 121
112TYRTYRGLYGLYAA212 - 259129 - 176
212TYRTYRGLYGLYBB212 - 259129 - 176
122LEULEUGLYGLYAA268 - 307185 - 224
222LEULEUGLYGLYBB268 - 307185 - 224
113GLUGLUASPASPAA308 - 368225 - 285
213GLUGLUASPASPBB308 - 368225 - 285
123PROPROVALVALAA388 - 397305 - 314
223PROPROVALVALBB388 - 397305 - 314
133ASNASNGLUGLUAA405 - 429322 - 346
233ASNASNGLUGLUBB405 - 429322 - 346
143VALVALGLUGLUAA434 - 501351 - 418
243VALVALGLUGLUBB434 - 501351 - 418

NCS ensembles :
ID
1
2
3
Detailstransient dimer

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Components

#1: Protein Serine/threonine-protein kinase Chk2 / Cds1


Mass: 48113.102 Da / Num. of mol.: 2 / Fragment: residues 84-502 / Mutation: K249R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHEK2, CHK2, RAD53 / Production host: Escherichia coli (E. coli)
References: UniProt: O96017, non-specific serine/threonine protein kinase

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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: 52.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1:1 ratio mix of protein solution (~12 mg/ml protein in 20 mM Tris-HCl, 150 mM NaCl, 10 mM dithiothreitol (DTT), 3% (v/v) glycerol, pH 8.0and well bifffer ( 50 mM Na2SO4 Sulfate, 14% (w/v) ...Details: 1:1 ratio mix of protein solution (~12 mg/ml protein in 20 mM Tris-HCl, 150 mM NaCl, 10 mM dithiothreitol (DTT), 3% (v/v) glycerol, pH 8.0and well bifffer ( 50 mM Na2SO4 Sulfate, 14% (w/v) PEG 3350). Crystals were flash frozen in crystallization buffer supplemented with 16-20 % (v/v) glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97922
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 20144 / % possible obs: 98.3 % / Redundancy: 4.96 % / Rsym value: 0.051

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GXC, 1A06

1gxc

1a06


Resolution: 3→12 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.855 / SU B: 38.384 / SU ML: 0.325 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.521 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1493 7.8 %RANDOM
Rwork0.244 ---
obs0.247 17738 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2--0.09 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6227 0 0 0 6227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226363
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.241.9678580
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8565757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1224.013299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.389151168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3631539
X-RAY DIFFRACTIONr_chiral_restr0.0880.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024741
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.22901
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.24291
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2226
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3590.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7011.253888
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9142.256159
X-RAY DIFFRACTIONr_scbond_it2.7222777
X-RAY DIFFRACTIONr_scangle_it4.3013.52421
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1927tight positional0.010.03
2704tight positional0.010.03
31333tight positional0.020.03
1927tight thermal3.0915
2704tight thermal4.9315
31333tight thermal4.8215
LS refinement shellResolution: 3→3.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.515 84 -
Rwork0.405 1024 -
obs--78.19 %
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)
110.47862.1578-3.41288.4221-3.20449.24140.087-0.08860.10770.15910.0408-0.28620.0231-0.1488-0.12780.0995-0.3294-0.0979-0.33990.0742-0.2009-12.140230.375929.9902
210.312-0.285-0.361710.6455-1.99447.1883-0.1415-0.0896-1.44490.97360.0451-1.57780.52130.93210.09650.225-0.0402-0.39810.09340.10810.558815.389830.091127.7949
38.69494.52351.0895.9714-1.08426.02920.06840.5409-1.0631-0.44950.3960.62680.5806-1.096-0.4644-0.037-0.2448-0.0305-0.0158-0.0673-0.024510.279850.19135.8403
49.18072.7294.27037.35222.20687.97890.2008-0.45761.32410.4679-0.39340.7196-0.0973-0.19910.19260.2223-0.1070.4421-0.00820.05850.4073-8.013760.183527.0735
54.39920.2323-0.37483.25810.60095.1987-0.13210.25490.1101-0.04690.06270.47010.1826-0.87180.0695-0.5743-0.0415-0.0378-0.38870.0816-0.666320.416974.891914.2171
64.27440.7917-0.56675.38750.49628.1536-0.27450.26120.552-0.42890.11981.2346-0.6346-0.92030.1547-0.07580.1189-0.02620.22530.28620.9522-18.81169.3032.4171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A89 - 207
2X-RAY DIFFRACTION2B89 - 207
3X-RAY DIFFRACTION3A208 - 305
4X-RAY DIFFRACTION4B208 - 305
5X-RAY DIFFRACTION5A306 - 501
6X-RAY DIFFRACTION6B306 - 501

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