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- PDB-3va4: Crystal structure of the mammalian MDC1 FHA domain complexed with... -

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Basic information

Entry
Database: PDB / ID: 3va4
TitleCrystal structure of the mammalian MDC1 FHA domain complexed with CHK2 pThr68 peptide
Components
  • Mediator of DNA damage checkpoint protein 1
  • Serine/threonine-protein kinase Chk2
KeywordsCELL CYCLE / FHA domain / DNA-damage / CHK2 and MDC1 dimerization
Function / homology
Function and homology information


SUMOylation of DNA damage response and repair proteins / G2/M DNA damage checkpoint / positive regulation of anoikis / Nonhomologous End-Joining (NHEJ) / mitotic DNA damage checkpoint signaling / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / response to glycoside / cellular response to bisphenol A / regulation of autophagosome assembly ...SUMOylation of DNA damage response and repair proteins / G2/M DNA damage checkpoint / positive regulation of anoikis / Nonhomologous End-Joining (NHEJ) / mitotic DNA damage checkpoint signaling / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / response to glycoside / cellular response to bisphenol A / regulation of autophagosome assembly / DNA replication checkpoint signaling / chromatin-protein adaptor activity / protein localization to site of double-strand break / mitotic intra-S DNA damage checkpoint signaling / thymocyte apoptotic process / cellular response to stress / regulation of protein catabolic process / negative regulation of DNA damage checkpoint / replicative senescence / signal transduction in response to DNA damage / mitotic spindle assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / DNA damage checkpoint signaling / regulation of signal transduction by p53 class mediator / histone reader activity / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Stabilization of p53 / protein catabolic process / G2/M DNA damage checkpoint / cellular response to gamma radiation / PML body / Regulation of TP53 Activity through Methylation / intrinsic apoptotic signaling pathway in response to DNA damage / G2/M transition of mitotic cell cycle / Regulation of TP53 Degradation / cellular response to xenobiotic stimulus / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / chromosome / protein autophosphorylation / Regulation of TP53 Activity through Phosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein stabilization / protein phosphorylation / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / ubiquitin protein ligase binding / DNA damage response / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / protein homodimerization activity / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / Regulator of Ty1 transposition protein 107 BRCT domain / Tumour Suppressor Smad4 - #20 / BRCT domain / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily ...: / Regulator of Ty1 transposition protein 107 BRCT domain / Tumour Suppressor Smad4 - #20 / BRCT domain / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / 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 / Mainly Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase Chk2 / Mediator of DNA damage checkpoint protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.54 Å
AuthorsWu, H.H. / Wu, P.Y. / Huang, K.F. / Kao, Y.Y. / Tsai, M.D.
CitationJournal: Biochemistry / Year: 2012
Title: Structural Delineation of MDC1-FHA Domain Binding with CHK2-pThr68.
Authors: Wu, H.H. / Wu, P.Y. / Huang, K.F. / Kao, Y.Y. / Tsai, M.D.
History
DepositionDec 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mediator of DNA damage checkpoint protein 1
C: Serine/threonine-protein kinase Chk2
B: Mediator of DNA damage checkpoint protein 1


Theoretical massNumber of molelcules
Total (without water)30,5293
Polymers30,5293
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-14 kcal/mol
Surface area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.508, 70.224, 101.335
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mediator of DNA damage checkpoint protein 1


Mass: 14589.714 Da / Num. of mol.: 2 / Fragment: N-terminal FHA domain (UNP RESIDUES 29-139)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Mouse / Gene: MDC1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5PSV9
#2: Protein/peptide Serine/threonine-protein kinase Chk2 / CHK2 checkpoint homolog / Cds1 homolog / Hucds1 / hCds1 / Checkpoint kinase 2


Mass: 1349.335 Da / Num. of mol.: 1 / Fragment: CHK2-pThr68 peptide (UNP RESIDUES 63-73) / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Homo sapiens (human) / References: UniProt: O96017
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 % sol: 25.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 1.26M (NH4)2SO4, 0.2M NaCl, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.54→57.72 Å / Num. all: 31096 / Num. obs: 30878 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 31.5
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3039 / Rsym value: 0.508 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.54→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.104 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20465 1546 5 %RANDOM
Rwork0.15925 ---
all0.1616 31042 --
obs0.1616 29179 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.648 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.54→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 0 153 1935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191833
X-RAY DIFFRACTIONr_angle_refined_deg2.2931.9872498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6655224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.37223.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.82715291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7671514
X-RAY DIFFRACTIONr_chiral_restr0.1710.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0221414
X-RAY DIFFRACTIONr_rigid_bond_restr7.85531833
X-RAY DIFFRACTIONr_sphericity_free20.219562
X-RAY DIFFRACTIONr_sphericity_bonded13.58451873
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 109 -
Rwork0.18 1951 -
obs--98.71 %
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)
11.00350.00970.34940.0132-0.09391.1976-0.0627-0.02590.08180.0007-0.0157-0.00410.03690.01010.07840.0307-0.0124-0.0080.0315-0.00160.011419.365133.651226.1557
20.90250.16430.02620.41030.01290.52730.0005-0.0240.0076-0.0565-0.0063-0.0373-0.0255-0.01690.00580.01190.00540.00770.00990.00170.027317.305136.36261.0532
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 137
2X-RAY DIFFRACTION1A201 - 263
3X-RAY DIFFRACTION2B28 - 135
4X-RAY DIFFRACTION2B201 - 279

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