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- PDB-3c1c: The effect of H3 K79 dimethylation and H4 K20 trimethylation on n... -

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Basic information

Entry
Database: PDB / ID: 3c1c
TitleThe effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure
Components
  • Histone 2, H2bf
  • Histone H2A type 1
  • Histone H3-like
  • Histone H4
  • Palindromic 146bp Human Alpha satellite DNA
KeywordsStructural PROTEIN/DNA / Nucleosome / chromatin / Histone H3 / trimethylation / histone modification / nucleosomal surface / nucleosomal array / Acetylation / Chromosomal protein / DNA-binding / Methylation / Nucleosome core / Nucleus / Phosphoprotein / Ubl conjugation / Structural PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Packaging Of Telomere Ends / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / HATs acetylate histones / Ub-specific processing proteases / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends ...Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Packaging Of Telomere Ends / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / HATs acetylate histones / Ub-specific processing proteases / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends / Deposition of new CENPA-containing nucleosomes at the centromere / E3 ubiquitin ligases ubiquitinate target proteins / : / PRC2 methylates histones and DNA / Condensation of Prophase Chromosomes / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / : / NoRC negatively regulates rRNA expression / : / Transcriptional regulation by small RNAs / : / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Estrogen-dependent gene expression / structural constituent of chromatin / nucleosome / 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 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 / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 H3.3C / Histone H2A type 1 / Histone H4 / Histone H3.2 / Histone H2B
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Xenopus tropicalis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsLu, X. / Simon, M. / Chodaparambil, J. / Hansen, J. / Shokat, K. / Luger, K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure.
Authors: Lu, X. / Simon, M.D. / Chodaparambil, J.V. / Hansen, J.C. / Shokat, K.M. / Luger, K.
History
DepositionJan 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_conn / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3-like
B: Histone H4
C: Histone H2A type 1
D: Histone 2, H2bf
E: Histone H3-like
F: Histone H4
G: Histone H2A type 1
H: Histone 2, H2bf
I: Palindromic 146bp Human Alpha satellite DNA
J: Palindromic 146bp Human Alpha satellite DNA


Theoretical massNumber of molelcules
Total (without water)198,90310
Polymers198,90310
Non-polymers00
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54960 Å2
ΔGint-362 kcal/mol
Surface area73430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.030, 110.080, 182.600
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-like /


Mass: 15316.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: Histone H3 / Production host: Escherichia coli (E. coli) / References: UniProt: P02302, UniProt: P84233*PLUS
#2: 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) / Gene: Histone H4 / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A type 1


Mass: 14008.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: Histone H2A / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#4: Protein Histone 2, H2bf /


Mass: 13808.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus (Silurana) tropicalis (tropical clawed frog)
Gene: hist2h2bf, TGas058p09.1-001 / Production host: Escherichia coli (E. coli) / References: UniProt: Q28D68

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DNA chain / Non-polymers , 2 types, 286 molecules IJ

#5: DNA chain Palindromic 146bp Human Alpha satellite DNA


Mass: 45054.844 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Manganese chloride, Potassium chloride, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1Manganese chloride11
2Potassium cacodylate11
3Potassium cacodylate12
4Potassium chloride12

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2
DetectorDetector: CCD / Date: Sep 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.15→53 Å / Num. obs: 34295 / % possible obs: 90 % / Observed criterion σ(F): 1452 / Observed criterion σ(I): 32813 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.7
Reflection shellResolution: 3.15→3.26 Å / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 3.8 / Num. unique all: 193527 / % possible all: 90

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AOI

1aoi


Resolution: 3.15→53 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 --Random
Rwork0.22 ---
obs-34295 90.8 %-
Refinement stepCycle: LAST / Resolution: 3.15→53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5966 5980 0 284 12230
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.382
X-RAY DIFFRACTIONc_bond_d0.008

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