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- PDB-5b1m: The mouse nucleosome structure containing H3.1 -

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Basic information

Entry
Database: PDB / ID: 5b1m
TitleThe mouse nucleosome structure containing H3.1
Components
  • DNA (146-MER)
  • Histone H2A type 1
  • Histone H2B type 3-A
  • Histone H3.1
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / chromatin / DNA binding / histone-fold / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


: / : / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / Assembly of the ORC complex at the origin of replication / Transcriptional regulation by small RNAs / chromatin organization => GO:0006325 / B-WICH complex positively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Deposition of new CENPA-containing nucleosomes at the centromere ...: / : / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / Assembly of the ORC complex at the origin of replication / Transcriptional regulation by small RNAs / chromatin organization => GO:0006325 / B-WICH complex positively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / Chromatin modifying enzymes / SUMOylation of chromatin organization proteins / DNA Damage/Telomere Stress Induced Senescence / Interleukin-7 signaling / G2/M DNA damage checkpoint / HDMs demethylate histones / Regulation of endogenous retroelements by KRAB-ZFP proteins / Senescence-Associated Secretory Phenotype (SASP) / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / Recognition and association of DNA glycosylase with site containing an affected purine / Metalloprotease DUBs / 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 / PKMTs methylate histone lysines / 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 / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / Oxidative Stress Induced Senescence / Ub-specific processing proteases / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A ...Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / 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 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2A type 1-B / Histone H2A type 1-B / Histone H4 / Histone H3.1 / H2B.U histone 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsUrahama, T. / Machida, S. / Horikoshi, N. / Osakabe, A. / Tachiwana, H. / Taguchi, H. / Kurumizaka, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (MEXT)25116002 Japan
the Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Cell Rep / Year: 2017
Title: Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis
Authors: Ueda, J. / Harada, A. / Urahama, T. / Machida, S. / Maehara, K. / Hada, M. / Makino, Y. / Nogami, J. / Horikoshi, N. / Osakabe, A. / Taguchi, H. / Tanaka, H. / Tachiwana, H. / Yao, T. / ...Authors: Ueda, J. / Harada, A. / Urahama, T. / Machida, S. / Maehara, K. / Hada, M. / Makino, Y. / Nogami, J. / Horikoshi, N. / Osakabe, A. / Taguchi, H. / Tanaka, H. / Tachiwana, H. / Yao, T. / Yamada, M. / Iwamoto, T. / Isotani, A. / Ikawa, M. / Tachibana, T. / Okada, Y. / Kimura, H. / Ohkawa, Y. / Kurumizaka, H. / Yamagata, K.
History
DepositionDec 8, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
D: Histone H2B type 3-A
E: Histone H3.1
F: Histone H4
G: Histone H2A type 1
H: Histone H2B type 3-A
I: DNA (146-MER)
J: DNA (146-MER)


Theoretical massNumber of molelcules
Total (without water)202,41110
Polymers202,41110
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56370 Å2
ΔGint-390 kcal/mol
Surface area72250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.715, 107.663, 168.342
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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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3.1


Mass: 15719.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Gene: Hist1h3a, H3a, Hist1h3g, H3.1-221, H3g, Hist1h3h, H3.1-291, H3h, Hist1h3i, H3.1-I, H3i
Plasmid: pHCE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P68433
#2: Protein Histone H4


Mass: 11676.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Gene: Hist1h4a, Hist1h4b, H4-53, Hist1h4c, H4-12, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4m, Hist2h4a, Hist2h4, Hist4h4
Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P62806
#3: Protein Histone H2A type 1


Mass: 14447.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Gene: Hist1h2ab, Hist1h2ac, Hist1h2ad, Hist1h2ae, Hist1h2ag, Hist1h2ai, Hist1h2an, Hist1h2ao
Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22752, UniProt: C0HKE1*PLUS
#4: Protein Histone H2B type 3-A


Mass: 14307.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hist3h2ba / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9D2U9

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DNA chain / Non-polymers , 2 types, 87 molecules IJ

#5: DNA chain DNA (146-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 DH5[alpha] (bacteria) / Strain (production host): DH5[alpha]
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: potassium cacodylate, potassium chloride, manganese chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 74131 / % possible obs: 96 % / Redundancy: 7 % / Biso Wilson estimate: 39.39 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.033 / Rrim(I) all: 0.095 / Χ2: 0.951 / Net I/av σ(I): 15.88 / Net I/σ(I): 9.3 / Num. measured all: 519592
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.34-2.423.60.48972090.6030.2710.5630.94594.4
2.42-2.525.40.46173270.7510.2010.5060.96696.3
2.52-2.646.50.38874220.8680.1520.4191.01297.1
2.64-2.776.60.31474140.920.1220.3381.05997
2.77-2.956.40.23373310.9560.0930.2521.05796
2.95-3.187.70.1774880.9840.0610.1811.0297.3
3.18-3.58.20.10574760.9930.0370.1120.93897.4
3.5-48.20.07374880.9960.0260.0780.92496.6
4-5.048.40.05474530.9970.0190.0570.92495.5
5.04-508.90.05675230.9970.0190.0590.75992.9

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Processing

Software
NameVersionClassification
HKL-2000705bdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AFA

3afa


Resolution: 2.34→39.593 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3693 5.03 %Ramdom selection
Rwork0.2114 69668 --
obs0.2138 73361 96.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.1 Å2 / Biso mean: 50.0698 Å2 / Biso min: 5.87 Å2
Refinement stepCycle: final / Resolution: 2.34→39.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6006 5980 0 85 12071
Biso mean---32.83 -
Num. residues----1048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912794
X-RAY DIFFRACTIONf_angle_d1.06818528
X-RAY DIFFRACTIONf_chiral_restr0.0542105
X-RAY DIFFRACTIONf_plane_restr0.0071335
X-RAY DIFFRACTIONf_dihedral_angle_d25.8216692
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.34-2.37080.33521070.27082596270394
2.3708-2.40330.31131310.25462641277295
2.4033-2.43760.30761580.2642629278796
2.4376-2.4740.30651310.25792653278496
2.474-2.51260.30771270.24732667279497
2.5126-2.55380.29641240.24562694281897
2.5538-2.59780.31441380.25142705284397
2.5978-2.64510.31311470.24562650279797
2.6451-2.69590.28821570.24782671282897
2.6959-2.75090.28841350.24472696283197
2.7509-2.81070.31281590.25182646280596
2.8107-2.87610.32391540.2452624277896
2.8761-2.9480.31211650.23952611277696
2.948-3.02770.28321470.24092709285697
3.0277-3.11680.30451370.24842720285797
3.1168-3.21730.32331540.24022700285498
3.2173-3.33220.28191390.22212712285198
3.3322-3.46560.2351490.20722708285797
3.4656-3.62320.23131370.20152699283697
3.6232-3.81410.27621330.19832725285897
3.8141-4.05280.2181560.19152682283897
4.0528-4.36540.21111390.17912692283196
4.3654-4.8040.23611500.18082680283095
4.804-5.49760.22821360.18372691282794
5.4976-6.92040.28541370.20592706284394
6.9204-39.59910.18531460.17362761290792

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