- PDB-3szm: STRUCTURE OF HUMAN MICROCEPHALIN (MCPH1) TANDEM BRCT DOMAINS IN C... -
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Basic information
Entry
Database: PDB / ID: 3szm
Title
STRUCTURE OF HUMAN MICROCEPHALIN (MCPH1) TANDEM BRCT DOMAINS IN COMPLEX WITH A GAMMA-H2AX PHOSPHOPEPTIDE
Components
Histone H2A.x
Microcephalin
Keywords
CELL CYCLE/Peptide / DNA REPAIR / CELL CYCLE-Peptide complex
Function / homology
Function and homology information
regulation of chromosome condensation / neuronal stem cell population maintenance / regulation of centrosome cycle / XY body / 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 ...regulation of chromosome condensation / neuronal stem cell population maintenance / regulation of centrosome cycle / XY body / 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 / Meiotic synapsis / positive regulation of DNA repair / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / meiotic cell cycle / DNA damage checkpoint signaling / PRC2 methylates histones and DNA / replication fork / condensed nuclear chromosome / male germ cell nucleus / Defective pyroptosis / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / double-strand break repair via homologous recombination / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / bone development / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / cellular response to gamma radiation / cerebral cortex development / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / cellular senescence / double-strand break repair / nucleosome / 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 / mitotic cell cycle / Processing of DNA double-strand break ends / histone binding / regulation of inflammatory response / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / damaged DNA binding / nuclear speck / protein heterodimerization activity / Amyloid fiber formation / centrosome / DNA damage response / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.0079 Å / Relative weight: 1
Reflection
Resolution: 2.63→50 Å / Num. obs: 59208 / % possible obs: 90.2 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.57
Reflection shell
Resolution: 2.63→2.74 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2 / % possible all: 97.8
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Processing
Software
Name
Version
Classification
HKL-2000
datacollection
DM
modelbuilding
PHENIX
(PHENIX.REFINE: 1.6.1_357)
refinement
HKL-2000
datareduction
HKL-2000
datascaling
DM
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→31.37 Å / SU ML: 0.4 / σ(F): 1.96 / Phase error: 26.08 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Rfree
0.252
572
1.01 %
Rwork
0.201
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obs
0.202
56418
89.7 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.43 Å2 / ksol: 0.38 e/Å3