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- PDB-2azm: Crystal structure of the MDC1 brct repeat in complex with the his... -

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Basic information

Entry
Database: PDB / ID: 2azm
TitleCrystal structure of the MDC1 brct repeat in complex with the histone tail of gamma-H2AX
Components
  • GAMMA-H2AX HISTONE
  • Mediator of DNA damage checkpoint protein 1
KeywordsCELL CYCLE / BRCT REPEAT / PROTEIN-PHOSPHOPEPTIDE COMPLEX / DNA DAMAGE
Function / homology
Function and homology information


DNA replication checkpoint signaling / protein localization to site of double-strand break / XY body / mitotic intra-S DNA damage checkpoint signaling / chromatin-protein adaptor activity / response to ionizing radiation / histone reader activity / SUMOylation of DNA damage response and repair proteins / site of DNA damage / Replacement of protamines by nucleosomes in the male pronucleus ...DNA replication checkpoint signaling / protein localization to site of double-strand break / XY body / mitotic intra-S DNA damage checkpoint signaling / chromatin-protein adaptor activity / response to ionizing radiation / histone reader activity / SUMOylation of DNA damage response and repair proteins / site of DNA damage / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / male germ cell nucleus / DNA damage checkpoint signaling / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Regulation of PD-L1(CD274) transcription / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / positive regulation of DNA repair / DNA methylation / Condensation of Prophase Chromosomes / condensed nuclear chromosome / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / replication fork / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / TP53 Regulates Transcription of DNA Repair Genes / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Transcriptional regulation by small RNAs / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Formation of the beta-catenin:TCF transactivating complex / meiotic cell cycle / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / RMTs methylate histone arginines / structural constituent of chromatin / nucleosome / double-strand break repair / nucleosome assembly / chromosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / heterochromatin formation / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / DNA recombination / histone binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / damaged DNA binding / nuclear body / nuclear speck / protein heterodimerization activity / Amyloid fiber formation / DNA repair / centrosome / DNA damage response / enzyme binding / DNA binding / extracellular exosome / nucleoplasm / nucleus
Similarity search - Function
: / Regulator of Ty1 transposition protein 107 BRCT domain / BRCT domain / BRCT domain / 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 / BRCT domain / BRCT domain / 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 / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H2AX / Mediator of DNA damage checkpoint protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.41 Å
AuthorsClapperton, J.A. / Stucki, M. / Mohammad, D. / Yaffe, M.B. / Jackson, S.P. / Smerdon, S.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: MDC1 Directly Binds Phosphorylated Histone H2AX to Regulate Cellular Responses to DNA Double-Strand Breaks
Authors: Stucki, M. / Clapperton, J.A. / Mohammad, D. / Yaffe, M.B. / Smerdon, S.J. / Jackson, S.P.
History
DepositionSep 12, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 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
C: GAMMA-H2AX HISTONE
D: GAMMA-H2AX HISTONE


Theoretical massNumber of molelcules
Total (without water)48,2404
Polymers48,2404
Non-polymers00
Water6,323351
1
A: Mediator of DNA damage checkpoint protein 1
C: GAMMA-H2AX HISTONE


Theoretical massNumber of molelcules
Total (without water)24,1202
Polymers24,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-7 kcal/mol
Surface area9900 Å2
MethodPISA
2
B: Mediator of DNA damage checkpoint protein 1
D: GAMMA-H2AX HISTONE


Theoretical massNumber of molelcules
Total (without water)24,1202
Polymers24,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-6 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.437, 75.609, 114.849
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: 22884.963 Da / Num. of mol.: 2 / Fragment: BRCT REPEAT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDC1 / Plasmid: PGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q14676
#2: Protein/peptide GAMMA-H2AX HISTONE / Histone H2AFX


Mass: 1235.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: GAMMA H2AX SYNTHETIC PEPTIDE / References: UniProt: P16104*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, NaCl, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.97852 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 23006 / Num. obs: 23006 / Redundancy: 12.6 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 17.4
Reflection shellResolution: 2.4→2.51 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.41→15 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.886 / SU B: 7.155 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.308 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 1177 5.1 %RANDOM
Rwork0.19058 ---
obs0.1936 21707 98.64 %-
all-23323 --
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: 27.541 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å20 Å2
2---1.57 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.41→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3081 0 0 351 3432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223157
X-RAY DIFFRACTIONr_angle_refined_deg1.3092.0074297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8265394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65722.713129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93215.058514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2891528
X-RAY DIFFRACTIONr_chiral_restr0.0850.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022406
X-RAY DIFFRACTIONr_nbd_refined0.1960.21547
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22122
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2293
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.226
X-RAY DIFFRACTIONr_mcbond_it0.82322044
X-RAY DIFFRACTIONr_mcangle_it1.40633234
X-RAY DIFFRACTIONr_scbond_it2.414.51232
X-RAY DIFFRACTIONr_scangle_it3.69561063
LS refinement shellResolution: 2.41→2.471 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 75 -
Rwork0.22 1295 -
obs--82.88 %

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