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- PDB-3uot: Crystal Structure of MDC1 FHA Domain in Complex with a Phosphoryl... -

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Basic information

Entry
Database: PDB / ID: 3uot
TitleCrystal Structure of MDC1 FHA Domain in Complex with a Phosphorylated Peptide from the MDC1 N-terminus
Components(Mediator of DNA damage checkpoint protein 1) x 2
KeywordsCELL CYCLE / FHA domain / DNA-damage / MDC1 dimerization
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 / focal adhesion / DNA repair / 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 ...: / 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 / SYNCHROTRON / SAD / Resolution: 1.8 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 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Database references
Revision 1.2Oct 16, 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

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Assembly

Deposited unit
A: Mediator of DNA damage checkpoint protein 1
B: Mediator of DNA damage checkpoint protein 1
D: Mediator of DNA damage checkpoint protein 1
E: Mediator of DNA damage checkpoint protein 1


Theoretical massNumber of molelcules
Total (without water)29,8314
Polymers29,8314
Non-polymers00
Water2,702150
1
A: Mediator of DNA damage checkpoint protein 1
D: Mediator of DNA damage checkpoint protein 1


Theoretical massNumber of molelcules
Total (without water)14,9162
Polymers14,9162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-8 kcal/mol
Surface area7520 Å2
MethodPISA
2
B: Mediator of DNA damage checkpoint protein 1
E: Mediator of DNA damage checkpoint protein 1


Theoretical massNumber of molelcules
Total (without water)14,9162
Polymers14,9162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-7 kcal/mol
Surface area6600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.485, 59.880, 72.081
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: 13505.397 Da / Num. of mol.: 2 / Fragment: N-terminal FHA domain (residues 19-138)
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: Protein/peptide Mediator of DNA damage checkpoint protein 1 / Nuclear factor with BRCT domains 1


Mass: 1410.259 Da / Num. of mol.: 2 / Fragment: Phosphorylated N-terminus (residues 1-10) / Mutation: A6(MSE) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14676
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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 Matthews: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.5
Details: 25% v/v ethanol, 0.1M sodium acetate pH 5.5, Microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.961 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 23, 2007
RadiationMonochromator: 0.87 / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.961 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. all: 24225 / Num. obs: 24225 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.037
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.315 / Num. unique all: 2515 / % possible all: 55.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.575 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24262 1172 5.1 %RANDOM
Rwork0.20489 ---
obs0.20687 21805 95.37 %-
all-21805 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.954 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2---1.64 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 0 150 2042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191947
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9882646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4855238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97223.44887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49815314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6921515
X-RAY DIFFRACTIONr_chiral_restr0.090.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0221473
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 41 -
Rwork0.331 974 -
obs--62.04 %
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)
12.24470.50380.74832.82720.06891.4435-0.0260.10170.0441-0.27150.0842-0.5090.02590.2387-0.05830.0518-0.00280.06520.0836-0.03230.1195-0.02934.0629.425
21.80884.41920.615511.70733.36284.2255-0.25560.0527-0.1581-0.40870.0914-0.2210.5312-0.13760.16420.2673-0.0193-0.03430.1816-0.02440.1726-1.8616.5219.736
32.4010.57920.15536.28451.72572.4845-0.20070.1581-0.0603-0.41510.1970.42190.0128-0.06720.00380.0475-0.0359-0.02940.0630.02340.0409-25.84926.49227.824
40.2365-1.38270.049211.31372.49022.46820.01690.06280.0558-0.6635-0.0105-0.3175-0.55480.2545-0.00640.2702-0.0408-0.06370.19540.11480.1263-25.23743.60420.209
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 135
2X-RAY DIFFRACTION2D2 - 9
3X-RAY DIFFRACTION3B28 - 134
4X-RAY DIFFRACTION4E3 - 9

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