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- PDB-3b6f: Nucleosome core particle treated with cisplatin -

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Basic information

Entry
Database: PDB / ID: 3b6f
TitleNucleosome core particle treated with cisplatin
Components
  • (147-MER DNA) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / nucleosome / chromatin / platinum adduct / cisplatin / anti-cancer / drug / Acetylation / Chromosomal protein / DNA-binding / Methylation / Nucleosome core / Nucleus / Phosphorylation / Ubl conjugation / STRUCTURAL PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus
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 H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.45 Å
AuthorsWu, B. / Davey, C.A.
Citation
Journal: Nat.Chem.Biol. / Year: 2008
Title: Site selectivity of platinum anticancer therapeutics
Authors: Wu, B. / Droge, P. / Davey, C.A.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution
Authors: Davey, C.A. / Sargent, D.F. / Luger, K. / Maeder, A.W. / Richmond, T.J.
History
DepositionOct 29, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: 147-MER DNA
J: 147-MER DNA
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,42711
Polymers199,37210
Non-polymers551
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59370 Å2
ΔGint-371 kcal/mol
Surface area76280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.327, 109.380, 180.585
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 , 2 types, 2 molecules IJ

#1: DNA chain 147-MER DNA


Mass: 45368.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
#2: DNA chain 147-MER DNA


Mass: 45359.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101

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Protein , 4 types, 8 molecules AEBFCGDH

#3: Protein Histone H3.2 / Histone H3


Mass: 15303.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P84233
#4: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P62799
#5: Protein Histone H2A / Histone H2A.1


Mass: 13907.163 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC494591 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#6: Protein Histone H2B 1.1 / H2B1.1 / Histone H2B.2


Mass: 13848.097 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P02281

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Non-polymers , 1 types, 1 molecules

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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn

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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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: MnCl2, KCl, K-Cacodylate, pH 6.0, vapor diffusion, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1MnCl211
2KCl11
3K-Cacodylate11
4MnCl212
5KCl12
6K-Cacodylate12

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.072 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 10, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 3.45→93.66 Å / Num. obs: 28162 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 5.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.45-3.647.50.4851.43058140980.485100
3.64-3.867.50.3092.22879438520.309100
3.86-4.127.40.2023.42727336700.202100
4.12-4.457.40.1325.12527733940.132100
4.45-4.887.40.0917.12327231480.091100
4.88-5.457.40.0728.52105728620.072100
5.45-6.37.30.06291853525380.062100
6.3-7.717.20.0529.31560721740.052100
7.71-10.916.80.04612.11143616740.04697.3
10.91-109.385.60.04713.741897520.04774.8

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
RefinementStarting model: PDB entry 1KX5

1kx5


Resolution: 3.45→93.66 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.833 / SU B: 49.488 / SU ML: 0.866 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.937 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.402 588 2.1 %RANDOM
Rwork0.33 ---
obs0.331 28106 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 185.185 Å2
Baniso -1Baniso -2Baniso -3
1-3.59 Å20 Å20 Å2
2---17.45 Å20 Å2
3---13.85 Å2
Refinement stepCycle: LAST / Resolution: 3.45→93.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6269 6021 1 0 12291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02113104
X-RAY DIFFRACTIONr_angle_refined_deg1.2452.5418946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3095781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37421.196276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.063151233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2541589
X-RAY DIFFRACTIONr_chiral_restr0.0660.22151
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027732
X-RAY DIFFRACTIONr_nbd_refined0.2260.26576
X-RAY DIFFRACTIONr_nbtor_refined0.3050.28090
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2598
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.22
X-RAY DIFFRACTIONr_mcbond_it0.6831.54002
X-RAY DIFFRACTIONr_mcangle_it1.24426295
X-RAY DIFFRACTIONr_scbond_it0.607312281
X-RAY DIFFRACTIONr_scangle_it1.0914.512651
LS refinement shellResolution: 3.45→3.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 55 -
Rwork0.416 2018 -
all-2073 -
obs--100 %

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