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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


negative regulation of tumor necrosis factor-mediated signaling pathway / 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 ...negative regulation of tumor necrosis factor-mediated signaling pathway / 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 / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / 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 / innate immune response in mucosa / 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 / lipopolysaccharide binding / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / UCH proteinases / antibacterial humoral response / 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 / 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) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / gene expression / killing of cells of another organism / Estrogen-dependent gene expression / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / protein-containing complex / extracellular space / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol
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 H2B type 1-J / Histone H4 / 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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