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Basic information

Entry
Database: PDB / ID: 3x1t
TitleCrystal structure of nucleosome core particle consisting of mouse testis specific histone variants H2aa and H2ba
Components
  • DNA (146-MER)
  • Histone H2A
  • Histone H2B type 1-A
  • Histone H3.1
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / Histone variants of h2a and h2b / reprogramming / chromatin / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / E3 ubiquitin ligases ubiquitinate target proteins / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / Metalloprotease DUBs / Recognition and association of DNA glycosylase with site containing an affected purine ...Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / E3 ubiquitin ligases ubiquitinate target proteins / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / Metalloprotease DUBs / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / HDACs deacetylate histones / PRC2 methylates histones and DNA / UCH proteinases / Processing of DNA double-strand break ends / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / sperm DNA condensation / Estrogen-dependent gene expression / mononuclear cell migration / Ub-specific processing proteases / female germ cell nucleus / nucleosome disassembly / plasminogen activation / chromosome organization / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / 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 / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / 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 / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / histone binding / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / chromosome, telomeric region / cadherin binding / inflammatory response / Amyloid fiber formation / protein heterodimerization activity / cell surface / protein-containing complex / DNA binding
Similarity search - Function
Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A ...Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / Histone H4 / Histone H3.1 / Histone H2B type 1-A / Histone H2A
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.808 Å
AuthorsSivaraman, P. / Kumarevel, T.S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming
Authors: Padavattan, S. / Shinagawa, T. / Hasegawa, K. / Kumasaka, T. / Ishii, S. / Kumarevel, T.
History
DepositionNov 27, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: DNA (146-MER)
J: DNA (146-MER)
A: Histone H3.1
B: Histone H4
C: Histone H2A
D: Histone H2B type 1-A
E: Histone H3.1
F: Histone H4
G: Histone H2A
H: Histone H2B type 1-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,91640
Polymers199,42310
Non-polymers1,49230
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60640 Å2
ΔGint-588 kcal/mol
Surface area73090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.771, 109.597, 181.597
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 1 types, 2 molecules IJ

#1: DNA chain DNA (146-MER)


Mass: 45053.855 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic (others)

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Protein , 4 types, 8 molecules AEBFCGDH

#2: Protein Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 15305.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#3: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#4: Protein Histone H2A


Mass: 13952.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CGP4
#5: Protein Histone H2B type 1-A / Histone H2B / testis / Testis-specific histone H2B


Mass: 14136.502 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P70696

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Non-polymers , 3 types, 143 molecules

#6: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Mn
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 60-70mM Kcl, 70-90mM MnCl2, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 28, 2012
RadiationMonochromator: S II / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. all: 51865 / Num. obs: 51865 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.128
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.72 / Num. unique all: 5066 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AOI

1aoi


Resolution: 2.808→34.96 Å / SU ML: 0.34 / σ(F): 1.35 / Phase error: 26.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 2628 5.08 %random
Rwork0.2095 ---
obs0.2124 51778 99.16 %-
all-51865 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.69 Å2 / Biso mean: 73.1979 Å2 / Biso min: 14.25 Å2
Refinement stepCycle: LAST / Resolution: 2.808→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6058 5980 30 113 12181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512849
X-RAY DIFFRACTIONf_angle_d0.74418606
X-RAY DIFFRACTIONf_chiral_restr0.0292116
X-RAY DIFFRACTIONf_plane_restr0.0031346
X-RAY DIFFRACTIONf_dihedral_angle_d29.1985306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8084-2.85950.34761340.27532322245691
2.8595-2.91440.32251270.25642561268899
2.9144-2.97390.27741350.25372569270499
2.9739-3.03850.33291300.25552564269499
3.0385-3.10920.29141380.25442566270499
3.1092-3.18690.28511300.240425672697100
3.1869-3.2730.29931430.23725492692100
3.273-3.36920.29081440.227925892733100
3.3692-3.47790.26161330.220125882721100
3.4779-3.6020.25651340.208725852719100
3.602-3.74610.23161560.202725872743100
3.7461-3.91640.27361520.209425732725100
3.9164-4.12260.27871400.195925922732100
4.1226-4.38040.24431340.189426192753100
4.3804-4.71790.23551480.200925962744100
4.7179-5.19130.31061240.198126482772100
5.1913-5.93930.2791210.217626752796100
5.9393-7.47080.30711630.217526522815100
7.4708-34.96270.20291420.17042748289098

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