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- PDB-3c1b: The effect of H3 K79 dimethylation and H4 K20 trimethylation on n... -

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Basic information

Entry
Database: PDB / ID: 3c1b
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 / Dimethylated histone / trimethylated histone / methylation / nucleosomal surface / histone modification / nucleosomal array / chromatin / Acetylation / Chromosomal protein / DNA-binding / Nucleosome core / Nucleus / Phosphoprotein / 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 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: 2.2 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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)198,99710
Polymers198,99710
Non-polymers00
Water14,178787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56050 Å2
ΔGint-379 kcal/mol
Surface area73450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.670, 109.830, 181.030
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: 15303.930 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: 11323.350 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, 789 molecules IJ

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


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


Mass: 18.015 Da / Num. of mol.: 787 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.4 %
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: Oct 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→43 Å / Num. obs: 106458 / % possible obs: 99 % / Observed criterion σ(F): 4.8 / Observed criterion σ(I): 10.2 / Rmerge(I) obs: 0.066
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 99 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.6 / % possible all: 99

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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: 2.2→43 Å / Cross valid method: throught / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.27 -random
Rwork0.24 --
obs-106458 -
Refinement stepCycle: LAST / Resolution: 2.2→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6061 5980 0 787 12828
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.247
X-RAY DIFFRACTIONc_bond_d0.006

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