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- PDB-1aoi: COMPLEX BETWEEN NUCLEOSOME CORE PARTICLE (H3,H4,H2A,H2B) AND 146 ... -

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Basic information

Entry
Database: PDB / ID: 1aoi
TitleCOMPLEX BETWEEN NUCLEOSOME CORE PARTICLE (H3,H4,H2A,H2B) AND 146 BP LONG DNA FRAGMENT
Components
  • HISTONE H2A
  • HISTONE H2B
  • HISTONE H3
  • HISTONE H4
  • PALINDROMIC 146 BP DNA REPEAT 8/9 FROM HUMAN X-CHROMOSOME ALPHA SATELLITE DNA
KeywordsDNA BINDING PROTEIN/DNA / NUCLEOSOME / CHROMATIN / HISTONE / PROTEIN DNA INTERACTION / NUCLEOPROTEIN / SUPERCOILED DNA / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / protein heterodimerization activity / DNA binding / 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 H3.3C / Histone H2A type 1 / Histone H4
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsLuger, K. / Maeder, A.W. / Richmond, R.K. / Sargent, D.F. / Richmond, T.J.
CitationJournal: Nature / Year: 1997
Title: Crystal structure of the nucleosome core particle at 2.8 A resolution.
Authors: Luger, K. / Mader, A.W. / Richmond, R.K. / Sargent, D.F. / Richmond, T.J.
History
DepositionJul 3, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 30, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: PALINDROMIC 146 BP DNA REPEAT 8/9 FROM HUMAN X-CHROMOSOME ALPHA SATELLITE DNA
J: PALINDROMIC 146 BP DNA REPEAT 8/9 FROM HUMAN X-CHROMOSOME ALPHA SATELLITE DNA
A: HISTONE H3
B: HISTONE H4
C: HISTONE H2A
D: HISTONE H2B
E: HISTONE H3
F: HISTONE H4
G: HISTONE H2A
H: HISTONE H2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,54716
Polymers184,21810
Non-polymers3306
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.040, 181.780, 110.120
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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DNA chain , 1 types, 2 molecules IJ

#1: DNA chain PALINDROMIC 146 BP DNA REPEAT 8/9 FROM HUMAN X-CHROMOSOME ALPHA SATELLITE DNA


Mass: 45053.855 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein , 4 types, 8 molecules AEBFCGDH

#2: Protein HISTONE H3


Mass: 13244.528 Da / Num. of mol.: 2 / Fragment: HISTONE H3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02302
#3: Protein HISTONE H4


Mass: 9990.770 Da / Num. of mol.: 2 / Fragment: HISTONE H4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog)
Description: SYNTHETIC GENE, OPTIMIZED CODON USAGE FOR ESCHERICHIA COLI;
Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#4: Protein HISTONE H2A


Mass: 12639.772 Da / Num. of mol.: 2 / Fragment: HISTONE H2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#5: Protein HISTONE H2B


Mass: 11179.959 Da / Num. of mol.: 2 / Fragment: HISTONE H2B / Mutation: A7P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281

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Non-polymers , 2 types, 19 molecules

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


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion
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: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 52487 / % possible obs: 99 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.056 / Rsym value: 3.6
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.132 / % possible all: 95
Reflection
*PLUS
Num. measured all: 297397

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Processing

Software
NameVersionClassification
LOCALmodel building
X-PLOR3.843refinement
IN-HOUSESOFTWAREdata reduction
IN-HOUSESOFTWAREdata scaling
IN-HOUSESOFTWAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2.8→25 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Details: BULK SOLVENT MODEL USED
RfactorNum. reflectionSelection details
Rfree0.302 -RANDOM
Rwork0.224 --
obs-51237 -
Solvent computationSolvent model: BULK SOLVENT MODEL USED
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6387 5980 6 13 12386
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
σ(F): 3 / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS

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