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Basic information

Entry
Database: PDB / ID: 3x1v
TitleCrystal structure of nucleosome core particle in the presence of histone variant involved in reprogramming
Components
  • DNA (146-MER)
  • Histone H2A type 1-B/E
  • Histone H2B type 1-A
  • Histone H3.1
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / nucleosome / chromatin / histone variant / reprogramming / 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) / 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 / 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) / 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 / 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 / sperm DNA condensation / Estrogen-dependent gene expression / mononuclear cell migration / 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 / Metalloprotease DUBs / 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 / UCH proteinases / nucleosome / heterochromatin formation / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / 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) / Oxidative Stress Induced Senescence / histone binding / gene expression / Estrogen-dependent gene expression / chromosome, telomeric region / Ub-specific processing proteases / cadherin binding / Amyloid fiber formation / inflammatory response / protein heterodimerization activity / negative regulation of cell population proliferation / cell surface / protein-containing complex
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 H2A type 1-B/E / Histone H4 / Histone H3.1 / Histone H2B type 1-A
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.921 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 28, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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 type 1-B/E
D: Histone H2B type 1-A
E: Histone H3.1
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,84435
Polymers199,58810
Non-polymers1,25725
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60060 Å2
ΔGint-533 kcal/mol
Surface area73390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.327, 108.471, 168.677
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) / Gene: H3.1 / Plasmid: PHCE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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) / Gene: H4 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P62805
#4: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14034.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2A / Plasmid: PHCE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04908
#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) / Gene: H2BA / Plasmid: PHCE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P70696

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Non-polymers , 3 types, 58 molecules

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


Mass: 54.938 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Mn
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 60-70 mM KCl, 70-90 mM MnCl2, Na-cocodylate, 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: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2012
RadiationMonochromator: Si II / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. all: 38723 / Num. obs: 38723 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.4 % / Rmerge(I) obs: 0.184

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Processing

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

1aoi


Resolution: 2.921→39.809 Å / SU ML: 0.39 / σ(F): 0 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 1905 5.02 %Random
Rwork0.1905 ---
obs0.194 37933 94.3 %-
all-38723 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.17 Å2 / Biso mean: 45.2655 Å2 / Biso min: 4.48 Å2
Refinement stepCycle: LAST / Resolution: 2.921→39.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6147 5980 25 33 12185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112962
X-RAY DIFFRACTIONf_angle_d1.34318747
X-RAY DIFFRACTIONf_chiral_restr0.062127
X-RAY DIFFRACTIONf_plane_restr0.0071362
X-RAY DIFFRACTIONf_dihedral_angle_d29.7035363
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9209-2.9940.37971100.2642108221879
2.994-3.07490.33191290.23922359248888
3.0749-3.16530.30391310.22682456258791
3.1653-3.26740.29631290.21952505263492
3.2674-3.38420.29791360.21612510264693
3.3842-3.51960.28011330.20322522265593
3.5196-3.67970.28741330.19012519265293
3.6797-3.87350.24341370.19322601273896
3.8735-4.1160.24031420.17622655279798
4.116-4.43340.25351420.17142677281998
4.4334-4.87880.24381420.17822691283398
4.8788-5.58310.24031410.18852740288199
5.5831-7.02790.27311470.210427922939100
7.0279-39.81250.18971530.14672893304699

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