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- PDB-3un0: Crystal Structure of MDC1 FHA Domain -

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Basic information

Entry
Database: PDB / ID: 3un0
TitleCrystal Structure of MDC1 FHA Domain
ComponentsMediator of DNA damage checkpoint protein 1
KeywordsCELL CYCLE / FHA domain / DNA-damage
Function / homology
Function and homology information


chromatin-protein adaptor activity / DNA replication checkpoint signaling / protein localization to site of double-strand break / mitotic intra-S DNA damage checkpoint signaling / positive regulation of transcription initiation by RNA polymerase II / SUMOylation of DNA damage response and repair proteins / histone reader activity / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint ...chromatin-protein adaptor activity / DNA replication checkpoint signaling / protein localization to site of double-strand break / mitotic intra-S DNA damage checkpoint signaling / positive regulation of transcription initiation by RNA polymerase II / SUMOylation of DNA damage response and repair proteins / histone reader activity / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / site of double-strand break / Processing of DNA double-strand break ends / nuclear body / DNA repair / focal adhesion / DNA damage response / 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 / BRCT domain profile. ...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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsClapperton, J.A. / Lloyd, J. / Haire, L.F. / Li, J. / Smerdon, S.J.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The molecular basis of ATM-dependent dimerization of the Mdc1 DNA damage checkpoint mediator.
Authors: Jungmichel, S. / Clapperton, J.A. / Lloyd, J. / Hari, F.J. / Spycher, C. / Pavic, L. / Li, J. / Haire, L.F. / Bonalli, M. / Larsen, D.H. / Lukas, C. / Lukas, J. / MacMillan, D. / Nielsen, M. ...Authors: Jungmichel, S. / Clapperton, J.A. / Lloyd, J. / Hari, F.J. / Spycher, C. / Pavic, L. / Li, J. / Haire, L.F. / Bonalli, M. / Larsen, D.H. / Lukas, C. / Lukas, J. / MacMillan, D. / Nielsen, M.L. / Stucki, M. / Smerdon, S.J.
History
DepositionNov 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Database references
Revision 1.2Feb 28, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,0129
Polymers25,3392
Non-polymers6727
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mediator of DNA damage checkpoint protein 1
hetero molecules

A: Mediator of DNA damage checkpoint protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0129
Polymers25,3392
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area2060 Å2
ΔGint-107 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.250, 54.711, 98.063
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 / Nuclear factor with BRCT domains 1


Mass: 12669.676 Da / Num. of mol.: 2 / Fragment: N-terminal FHA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDC1, KIAA0170, NFBD1 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q14676
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 1.87 Å3/Da / Density % sol: 34.08 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.6
Details: 1.32M ammonium sulfate, 0.05M sodium acetate pH 4.6, 5% v/v methyl-pentanediol, Microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromator: 0 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 9055 / Num. obs: 9055 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.8 / Redundancy: 3 % / Rmerge(I) obs: 0.084
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.4 / Num. unique all: 992 / % possible all: 90.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→15.03 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 19.14 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26095 393 4.7 %RANDOM
Rwork0.20649 ---
obs0.20915 7988 94.05 %-
all-7988 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.343 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---1.06 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 35 79 1802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191774
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.9962415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6815216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46623.02676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.64215293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0791514
X-RAY DIFFRACTIONr_chiral_restr0.0860.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0221332
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 20 -
Rwork0.282 495 -
obs--92.29 %
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)
12.9127-0.1056-0.35432.4692-0.67134.0686-0.0976-0.1455-0.0559-0.0588-0.0229-0.08790.26480.15150.12060.09650.03550.01550.01820.00780.01312.382-14.89513.693
23.4906-0.4548-0.06372.7335-0.18223.43540.021-0.05130.08960.1572-0.0191-0.02870.1768-0.0292-0.00180.02570.0042-0.01310.03230.0060.06060.0217.6079.985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 134
2X-RAY DIFFRACTION2B27 - 133

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