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- PDB-3u3z: Structure of human microcephalin (MCPH1) tandem BRCT domains in c... -

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Basic information

Entry
Database: PDB / ID: 3u3z
TitleStructure of human microcephalin (MCPH1) tandem BRCT domains in complex with an H2A.X peptide phosphorylated at Ser139 and Tyr142
Components
  • Histone H2A.X peptide
  • Microcephalin
KeywordsCELL CYCLE / DNA repair / cell cycle regulation
Function / homology
Function and homology information


regulation of chromosome condensation / neuronal stem cell population maintenance / regulation of centrosome cycle / XY body / chromatin-protein adaptor activity / protein localization to site of double-strand break / protein localization to centrosome / response to ionizing radiation / establishment of mitotic spindle orientation / site of DNA damage ...regulation of chromosome condensation / neuronal stem cell population maintenance / regulation of centrosome cycle / XY body / chromatin-protein adaptor activity / protein localization to site of double-strand break / protein localization to centrosome / response to ionizing radiation / establishment of mitotic spindle orientation / site of DNA damage / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / 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 / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / positive regulation of DNA repair / Assembly of the ORC complex at the origin of replication / DNA damage checkpoint signaling / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / replication fork / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / condensed nuclear chromosome / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / meiotic cell cycle / male germ cell nucleus / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / bone development / G2/M DNA damage checkpoint / cerebral cortex development / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / heterochromatin formation / double-strand break repair / mitotic cell cycle / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / regulation of inflammatory response / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / Oxidative Stress Induced Senescence / histone binding / Estrogen-dependent gene expression / damaged DNA binding / nuclear speck / Amyloid fiber formation / protein heterodimerization activity / DNA damage response / centrosome / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Microcephalin-like / Microcephalin, mammal / Microcephalin protein / twin BRCT domain / BRCT domain / BRCT domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily ...Microcephalin-like / Microcephalin, mammal / Microcephalin protein / twin BRCT domain / BRCT domain / BRCT domain / breast cancer carboxy-terminal domain / 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 / Microcephalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSingh, N. / Thompson, J.R. / Heroux, A. / Mer, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Dual recognition of phosphoserine and phosphotyrosine in histone variant H2A.X by DNA damage response protein MCPH1.
Authors: Singh, N. / Basnet, H. / Wiltshire, T.D. / Mohammad, D.H. / Thompson, J.R. / Heroux, A. / Botuyan, M.V. / Yaffe, M.B. / Couch, F.J. / Rosenfeld, M.G. / Mer, G.
History
DepositionOct 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 19, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microcephalin
B: Histone H2A.X peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8194
Polymers22,6352
Non-polymers1842
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-11 kcal/mol
Surface area9920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.689, 46.537, 55.778
Angle α, β, γ (deg.)90.00, 97.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Microcephalin


Mass: 21949.551 Da / Num. of mol.: 1
Fragment: Tandem BRCT domains (BRCT2-BRCT3, UNP residues 640-835)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCPH1 / Plasmid: PTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 ROSETTA (DE3) / References: UniProt: Q8NEM0
#2: Protein/peptide Histone H2A.X peptide


Mass: 685.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P16104*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 22% PEG3350, 0.03 M citric acid, 0.07 M Bis-Tris-propane, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2010
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 29928 / % possible obs: 96.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 25.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.3 / % possible all: 80.1

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(PHENIX.REFINE: 1.6.1_357)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SZM

3szm


Resolution: 1.5→23.79 Å / SU ML: 0.16 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.171 517 1.73 %
Rwork0.129 --
obs0.129 29928 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 24.9061 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→23.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 12 279 1801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051641
X-RAY DIFFRACTIONf_angle_d1.0712256
X-RAY DIFFRACTIONf_dihedral_angle_d14.007620
X-RAY DIFFRACTIONf_chiral_restr0.057254
X-RAY DIFFRACTIONf_plane_restr0.005281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.65410.20091100.14867036X-RAY DIFFRACTION94
1.6541-1.89330.20271350.11947385X-RAY DIFFRACTION99
1.8933-2.3850.16491420.10327509X-RAY DIFFRACTION100
2.385-23.7910.15721300.1347481X-RAY DIFFRACTION98

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