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- PDB-1p3b: Crystallographic Studies of Nucleosome Core Particles containing ... -

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Basic information

Entry
Database: PDB / ID: 1p3b
TitleCrystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants
Components
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • Palindromic 146bp Human Alpha-Satellite DNA fragment
KeywordsSTRUCTURAL PROTEIN/DNA / Sin mutants / Nucleosome Core Particle / chromatin / protein/DNA interaction / 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 / : / :
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMuthurajan, U.M. / Bao, Y. / Forsberg, L.J. / Edayathumangalam, R.S. / Dyer, P.N. / White, C.L. / Luger, K.
CitationJournal: EMBO J. / Year: 2004
Title: Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions
Authors: Muthurajan, U.M. / Bao, Y. / Forsberg, L.J. / Edayathumangalam, R.S. / Dyer, P.N. / White, C.L. / Luger, K.
History
DepositionApr 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Palindromic 146bp Human Alpha-Satellite DNA fragment
J: Palindromic 146bp Human Alpha-Satellite DNA fragment
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B


Theoretical massNumber of molelcules
Total (without water)198,78410
Polymers198,78410
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.180, 109.520, 182.441
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#2: Protein Histone H3


Mass: 15363.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Variant (production host): BL21 DE3 plysS / References: UniProt: Q7ZT64, UniProt: P84233*PLUS
#3: Protein Histone H4


Mass: 11177.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Variant (production host): BL21 DE3 plysS / References: UniProt: P62799
#4: Protein Histone H2A


Mass: 13962.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Variant (production host): BL21 DE3 plysS / References: UniProt: Q7ZT66, UniProt: P06897*PLUS
#5: Protein Histone H2B


Mass: 13834.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Variant (production host): BL21 DE3 plysS / References: UniProt: P02281

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DNA chain / Non-polymers , 2 types, 166 molecules IJ

#1: DNA chain Palindromic 146bp Human Alpha-Satellite DNA fragment


Mass: 45054.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pUC / Production host: Escherichia coli (E. coli) / Variant (production host): HB 101
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1MnCl211
2KCl11
3Potassium cacodylate11
4MnCl212
5KCl12
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion / Details: Luger, K., (1997) Nature, 389, 251.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
14 mg/mlprotein1drop
250 mM1dropKCl
370-75 mM1dropMnCl2
420 mMpotassium cacodylate1droppH6.0
540-46 mM1reservoirMnCl2
635-40 mM1reservoirKCl
720 mMpotassium cacodylate1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 6, 2000 / Details: Mirrors
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→35 Å / Num. obs: 43495 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.98 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.3
Reflection shellResolution: 3→3.07 Å / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 43674 / % possible obs: 99.9 %
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AOI

1aoi


Resolution: 3→35 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1275 3.1 %Random
Rwork0.219 ---
all-42018 --
obs-40743 97 %-
Refinement stepCycle: LAST / Resolution: 3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5989 5980 0 164 12133
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_d1.19
X-RAY DIFFRACTIONc_angle_deg1.19
Refinement
*PLUS
Highest resolution: 3 Å / Rfactor Rfree: 0.29 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_d
LS refinement shell
*PLUS
Rfactor Rfree: 0.4 / Rfactor Rwork: 0.34

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