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- PDB-3wkj: The nucleosome containing human TSH2B -

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Basic information

Entry
Database: PDB / ID: 3wkj
TitleThe nucleosome containing human TSH2B
Components
  • DNA (145-MER)
  • Histone H2A type 1-B/E
  • Histone H2B type 1-A
  • Histone H3.1
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / histone variant / histone-fold / DNA binding protein / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


sperm DNA condensation / 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 ...sperm DNA condensation / 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 / E3 ubiquitin ligases ubiquitinate target proteins / 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 / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsUrahama, T. / Horikoshi, N. / Osakabe, A. / Tachiwana, H. / Kurumizaka, H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structure of human nucleosome containing the testis-specific histone variant TSH2B.
Authors: Urahama, T. / Horikoshi, N. / Osakabe, A. / Tachiwana, H. / Kurumizaka, H.
History
DepositionOct 22, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
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
I: DNA (145-MER)
J: DNA (145-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,17419
Polymers202,75710
Non-polymers4179
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56920 Å2
ΔGint-479 kcal/mol
Surface area71310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.037, 109.926, 182.961
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: 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: 15719.445 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
#2: Protein Histone H4


Mass: 11676.703 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
#3: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14447.825 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
#4: Protein Histone H2B type 1-A / Histone H2B / testis / TSH2B.1 / Testis-specific histone H2B


Mass: 14480.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BA, TSH2B / Plasmid: pHCE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96A08

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DNA chain , 1 types, 2 molecules IJ

#5: DNA chain DNA (145-MER)


Mass: 45053.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEM-T Easy / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha

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Non-polymers , 3 types, 110 molecules

#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 14, 2011
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 54290 / Num. obs: 53677 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 71.115 Å2 / Rsym value: 0.079 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.8-2.96.64.348560.504190.9
2.9-3.027.36.153410.3931100
3.02-3.157.48.953890.2731100
3.15-3.327.513.253370.1881100
3.32-3.537.520.353660.1251100
3.53-3.87.528.953980.0871100
3.8-4.187.539.254160.0631100
4.18-4.797.449.554680.0611100
4.79-6.036.950.354780.0671100
6.03-50760.956280.038198.1

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AFA

3afa


Resolution: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2907 2722 RANDOM
Rwork0.2351 --
all0.2865 53868 -
obs0.2445 53572 -
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5977 5939 9 101 12026
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.15974
X-RAY DIFFRACTIONc_bond_d0.007345
X-RAY DIFFRACTIONc_dihedral_angle_d20.33058
X-RAY DIFFRACTIONc_improper_angle_d1.04195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
2.8-2.90.41142730.3516X-RAY DIFFRACTION486110
2.9-3.020.3692420.3278X-RAY DIFFRACTION504210
3.02-3.150.32682980.2864X-RAY DIFFRACTION502710
3.15-3.320.32542990.294X-RAY DIFFRACTION504310
3.32-3.530.34662580.2842X-RAY DIFFRACTION506910
3.53-3.80.29432450.2559X-RAY DIFFRACTION511810
3.8-4.180.30212700.2387X-RAY DIFFRACTION509410
4.18-4.790.24512790.2031X-RAY DIFFRACTION514410
4.79-6.030.26232760.2218X-RAY DIFFRACTION516810
6.03-500.25482820.2097X-RAY DIFFRACTION528410

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