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- PDB-3va1: Crystal structure of the mammalian MDC1 FHA domain -

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Basic information

Entry
Database: PDB / ID: 3va1
TitleCrystal structure of the mammalian MDC1 FHA domain
ComponentsMediator of DNA damage checkpoint protein 1
KeywordsCELL CYCLE / FHA domain / DNA-damage / MDC1 dimerization
Function / homology
Function and homology information


SUMOylation of DNA damage response and repair proteins / G2/M DNA damage checkpoint / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA replication checkpoint signaling / protein localization to site of double-strand break / positive regulation of transcription initiation by RNA polymerase II / histone reader activity / chromosome ...SUMOylation of DNA damage response and repair proteins / G2/M DNA damage checkpoint / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA replication checkpoint signaling / protein localization to site of double-strand break / positive regulation of transcription initiation by RNA polymerase II / histone reader activity / chromosome / site of double-strand break / nuclear body / cell cycle / DNA repair / focal adhesion / nucleoplasm / nucleus
Similarity search - Function
Regulator of Ty1 transposition protein 107 BRCT domain / Tumour Suppressor Smad4 - #20 / BRCT domain, a BRCA1 C-terminus 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 ...Regulator of Ty1 transposition protein 107 BRCT domain / Tumour Suppressor Smad4 - #20 / BRCT domain, a BRCA1 C-terminus 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mediator of DNA damage checkpoint protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.74 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 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mediator of DNA damage checkpoint protein 1
B: Mediator of DNA damage checkpoint protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3724
Polymers29,1792
Non-polymers1922
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-5 kcal/mol
Surface area10690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.076, 48.590, 134.182
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) / Gene: Mdc1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5PSV9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.07 Å3/Da / Density % sol: 40.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.26M (NH4)2SO4, 0.2M Li2SO4, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 31, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→67.09 Å / Num. all: 25452 / Num. obs: 25045 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 38.9
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2386 / Rsym value: 0.498 / % possible all: 96

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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: 1.74→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.31 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27176 1265 5.1 %RANDOM
Rwork0.18861 ---
all0.19273 25501 --
obs0.19273 23441 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.364 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å20 Å2
2--2.38 Å2-0 Å2
3----2.11 Å2
Refinement stepCycle: LAST / Resolution: 1.74→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 10 146 1831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191723
X-RAY DIFFRACTIONr_angle_refined_deg2.0551.9822346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9523.15876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10315276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2271514
X-RAY DIFFRACTIONr_chiral_restr0.1380.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0221336
X-RAY DIFFRACTIONr_rigid_bond_restr7.10531723
X-RAY DIFFRACTIONr_sphericity_free23.092565
X-RAY DIFFRACTIONr_sphericity_bonded13.59651756
LS refinement shellResolution: 1.745→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 77 -
Rwork0.275 1411 -
obs-1616 87.32 %
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)
11.66060.2605-0.76991.71860.171.76890.1204-0.19870.0860.0812-0.044-0.0165-0.10330.0948-0.07650.0231-0.01440.020.0722-0.00530.02531.44796.166424.1078
22.08420.13940.04732.0534-0.41622.86130.0440.0393-0.2525-0.3692-0.06360.08710.2567-0.12490.01950.1060.0093-0.01210.031-0.00630.0401-13.0547-0.5185.6736
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 135
2X-RAY DIFFRACTION1A201 - 383
3X-RAY DIFFRACTION2B28 - 134
4X-RAY DIFFRACTION2B201 - 363

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