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- PDB-4ym6: Crystal structure of the human nucleosome containing 6-4PP (outside) -

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Basic information

Entry
Database: PDB / ID: 4ym6
TitleCrystal structure of the human nucleosome containing 6-4PP (outside)
Components
  • 145-MER DNA
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / 6-4 photoproduct / nucleosome / histone / DNA binding / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / negative regulation of tumor necrosis factor-mediated signaling pathway / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine ...protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / negative regulation of tumor necrosis factor-mediated signaling pathway / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / arachidonate metabolic process / Chromatin modifying enzymes / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / lipopolysaccharide binding / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / heterochromatin formation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / E3 ubiquitin ligases ubiquitinate target proteins / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / gene expression / antibacterial humoral response / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding / cytosol
Similarity search - Function
Histone, subunit A / Histone, subunit A / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / Centromere kinetochore component CENP-T histone fold ...Histone, subunit A / Histone, subunit A / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / Centromere kinetochore component CENP-T histone fold / 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 / 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/E / Histone H2B type 1-J / Arachidonate 15-lipoxygenase / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.514 Å
AuthorsOsakabe, A. / Tachiwana, H. / Kagawa, W. / Horikoshi, N. / Matsumoto, S. / Hasegawa, M. / Matsumoto, N. / Toga, T. / Yamamoto, J. / Hanaoka, F. ...Osakabe, A. / Tachiwana, H. / Kagawa, W. / Horikoshi, N. / Matsumoto, S. / Hasegawa, M. / Matsumoto, N. / Toga, T. / Yamamoto, J. / Hanaoka, F. / Thoma, N.H. / Sugasawa, K. / Iwai, S. / Kurumizaka, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25250023 Japan
Ministry of Education, Culture, Sports, Science and Technology25131720 Japan
Ministry of Education, Culture, Sports, Science and Technology25116002 Japan
CitationJournal: Sci Rep / Year: 2015
Title: Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome
Authors: Osakabe, A. / Tachiwana, H. / Kagawa, W. / Horikoshi, N. / Matsumoto, S. / Hasegawa, M. / Matsumoto, N. / Toga, T. / Yamamoto, J. / Hanaoka, F. / Thoma, N.H. / Sugasawa, K. / Iwai, S. / Kurumizaka, H.
History
DepositionMar 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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-B/E
D: Histone H2B type 1-J
E: Histone H3.1
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
I: 145-MER DNA
J: 145-MER DNA


Theoretical massNumber of molelcules
Total (without water)202,23110
Polymers202,23110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57040 Å2
ΔGint-380 kcal/mol
Surface area72160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.713, 109.483, 178.214
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain C and (resseq 15:118 )
21chain G and (resseq 15:118 )
12chain A and (resseq 38:134 )
22chain E and (resseq 38:134 )
13chain D and (resseq 30:121 )
23chain H and (resseq 30:121 )
14chain B and (resseq 25:102 )
24chain F and (resseq 25:102 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain C and (resseq 15:118 )C0
211chain G and (resseq 15:118 )G0
112chain A and (resseq 38:134 )A0
212chain E and (resseq 38:134 )E0
113chain D and (resseq 30:121 )D0
213chain H and (resseq 30:121 )H0
114chain B and (resseq 25:102 )B0
214chain F and (resseq 25:102 )F0

NCS ensembles :
ID
1
2
3
4

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Components

#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: HIST1H3A / Plasmid: pUC19 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: HIST1H4A / 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: HIST1H2AB / Plasmid: pUC19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04908
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14217.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ / Plasmid: pUC19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06899
#5: DNA chain 145-MER DNA


Mass: 45053.859 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: 2.55 Å3/Da / Density % sol: 51.76 %
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: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 30, 2010
RadiationMonochromator: Rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 26130 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 103.73 Å2 / Rmerge(I) obs: 0.096 / Χ2: 1.818 / Net I/av σ(I): 28.444 / Net I/σ(I): 9.3 / Num. measured all: 174199
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
3.5-3.636.90.5514.20525661.15100
3.63-3.776.90.39625841.20899.9
3.77-3.946.90.325781.237100
3.94-4.156.90.2325821.333100
4.15-4.416.90.1625941.46299.9
4.41-4.756.90.12326171.679100
4.75-5.236.80.11626122.14599.9
5.23-5.986.50.11526152.59799.8
5.98-7.536.40.07826762.86999.9
7.53-505.60.04327062.77996.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AFA

3afa


Resolution: 3.514→29.831 Å / FOM work R set: 0.7664 / SU ML: 0.52 / Cross valid method: NONE / σ(F): 0 / Phase error: 29.42 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2868 1286 5.08 %Random selection
Rwork0.2441 24009 --
obs0.2464 25295 95.83 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.706 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso max: 277.64 Å2 / Biso mean: 151.66 Å2 / Biso min: 63.2 Å2
Baniso -1Baniso -2Baniso -3
1-20.9974 Å2-0 Å20 Å2
2---44.8744 Å2-0 Å2
3---23.877 Å2
Refinement stepCycle: final / Resolution: 3.514→29.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6027 5980 0 0 12007
Num. residues----1048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01913494
X-RAY DIFFRACTIONf_angle_d1.33618563
X-RAY DIFFRACTIONf_chiral_restr0.0682108
X-RAY DIFFRACTIONf_plane_restr0.0041342
X-RAY DIFFRACTIONf_dihedral_angle_d29.1885284
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C806X-RAY DIFFRACTIONPOSITIONAL0.051
12G806X-RAY DIFFRACTIONPOSITIONAL0.051
21A801X-RAY DIFFRACTIONPOSITIONAL0.06
22E801X-RAY DIFFRACTIONPOSITIONAL0.06
31D719X-RAY DIFFRACTIONPOSITIONAL0.049
32H719X-RAY DIFFRACTIONPOSITIONAL0.049
41B619X-RAY DIFFRACTIONPOSITIONAL0.058
42F619X-RAY DIFFRACTIONPOSITIONAL0.058
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5141-3.65460.32151270.27352248237582
3.6546-3.82060.33141210.26572531265292
3.8206-4.02150.2661420.25442594273695
4.0215-4.27280.25671250.24252688281397
4.2728-4.60160.27061520.21312744289699
4.6016-5.06270.27071640.235927372901100
5.0627-5.79060.3531440.274227812925100
5.7906-7.2780.31431610.285428092970100
7.278-29.83250.26351500.22042877302798

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