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- PDB-3shv: Crystal structure of human MCPH1 tandem BRCT domains-gamma H2AX c... -

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Basic information

Entry
Database: PDB / ID: 3shv
TitleCrystal structure of human MCPH1 tandem BRCT domains-gamma H2AX complex
Components
  • Histone H2A.x
  • Microcephalin
KeywordsCELL CYCLE / tandem brct domains H2AX
Function / homology
Function and homology information


protein localization to site of double-strand break / XY body / chromatin-protein adaptor activity / response to ionizing radiation / male germ cell nucleus / DNA damage checkpoint signaling / 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 ...protein localization to site of double-strand break / XY body / chromatin-protein adaptor activity / response to ionizing radiation / male germ cell nucleus / DNA damage checkpoint signaling / 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 / replication fork / Deposition of new CENPA-containing nucleosomes at the centromere / positive regulation of DNA repair / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / 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 / site of DNA damage / condensed nuclear chromosome / DNA methylation / Condensation of Prophase Chromosomes / 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 / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Transcriptional regulation by small RNAs / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / cerebral cortex development / 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 / Formation of the beta-catenin:TCF transactivating complex / 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 / double-strand break repair / structural constituent of chromatin / nucleosome / Regulation of PD-L1(CD274) transcription / mitotic cell cycle / site of double-strand break / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / 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 / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / DNA recombination / heterochromatin formation / histone binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / damaged DNA binding / nuclear speck / protein heterodimerization activity / Amyloid fiber formation / centrosome / DNA damage response / negative regulation of transcription by RNA polymerase II / enzyme binding / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus
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 / molecular replacement / Resolution: 2.1 Å
AuthorsShao, Z.H. / Li, F.D. / Yan, W.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Specific recognition of phosphorylated tail of H2AX by the tandem BRCT domains of MCPH1 revealed by complex structure
Authors: Shao, Z.H. / Li, F.D. / Sy, S.M.-H. / Yan, W. / Zhang, Z. / Gong, D. / Wen, B. / Huen, M.S.Y. / Gong, Q. / Wu, J. / Shi, Y.
History
DepositionJun 17, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microcephalin
B: Microcephalin
C: Histone H2A.x
D: Histone H2A.x


Theoretical massNumber of molelcules
Total (without water)48,2164
Polymers48,2164
Non-polymers00
Water3,279182
1
A: Microcephalin
C: Histone H2A.x


Theoretical massNumber of molelcules
Total (without water)24,1082
Polymers24,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-7 kcal/mol
Surface area10220 Å2
MethodPISA
2
B: Microcephalin
D: Histone H2A.x


Theoretical massNumber of molelcules
Total (without water)24,1082
Polymers24,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-7 kcal/mol
Surface area10140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.772, 132.860, 31.534
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Microcephalin


Mass: 22872.615 Da / Num. of mol.: 2 / Fragment: residues 639-835
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCPH1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NEM0
#2: Protein/peptide Histone H2A.x


Mass: 1235.236 Da / Num. of mol.: 2 / Fragment: residues in UNP 134-143 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P16104
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS SEQUENCE IS FROM GENBANK NP_078872.2 MICROCEPHALIN ISOFORM 1. MICROCEPHALIN HAS A NATURAL ...THIS SEQUENCE IS FROM GENBANK NP_078872.2 MICROCEPHALIN ISOFORM 1. MICROCEPHALIN HAS A NATURAL VARIATIONS AT RESIDUE 761 POSITION IN UNIPROT DATABASE.

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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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Sodium acetate trihydrate, 100mM TRIS hydrochloride(pH 8.5), 30%(w/v) PEG4000 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2010
RadiationMonochromator: plane grating / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 31233 / Num. obs: 31077 / % possible obs: 99.5 % / Observed criterion σ(F): 3.1 / Observed criterion σ(I): 3.1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.064 / Χ2: 0.85 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.144.30.3514440.704197.8
2.14-2.184.70.33115170.762199.5
2.18-2.224.90.30915430.7181100
2.22-2.2650.27315320.821197.5
2.26-2.315.40.22714820.7621100
2.31-2.375.40.19415250.7741100
2.37-2.425.40.17415760.772199
2.42-2.495.60.16315000.793199.7
2.49-2.565.50.14615320.791100
2.56-2.655.50.11615520.83199.2
2.65-2.745.60.10515310.9041100
2.74-2.855.50.08815720.9091100
2.85-2.985.50.07115280.927199.7
2.98-3.145.40.05815951.0551100
3.14-3.335.50.05315401.067199.9
3.33-3.595.40.0515810.9511100
3.59-3.955.30.05215920.927199.7
3.95-4.525.10.04815920.774199.3
4.52-5.75.20.04215970.774199.6
5.7-504.80.03217460.882199

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.53 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.08 Å
Translation2.5 Å45.08 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SHT

3sht


Resolution: 2.1→45.08 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.2394 / WRfactor Rwork: 0.1959 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8437 / SU B: 4.066 / SU ML: 0.111 / SU R Cruickshank DPI: 0.1851 / SU Rfree: 0.1709 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 1564 5 %RANDOM
Rwork0.1966 ---
obs0.1988 31018 99.5 %-
all-31233 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.65 Å2 / Biso mean: 33.1432 Å2 / Biso min: 11.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3048 0 0 182 3230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223112
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.974245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1715386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75723.621116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38515.058513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0371514
X-RAY DIFFRACTIONr_chiral_restr0.0970.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0222308
X-RAY DIFFRACTIONr_mcbond_it0.9171.51954
X-RAY DIFFRACTIONr_mcangle_it1.73923176
X-RAY DIFFRACTIONr_scbond_it2.5631158
X-RAY DIFFRACTIONr_scangle_it4.1454.51069
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 115 -
Rwork0.207 2062 -
all-2177 -
obs--98.33 %

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