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- PDB-4xzq: Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acety... -

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Basic information

Entry
Database: PDB / ID: 4xzq
TitleNucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis
Components
  • (DNA (147-MER)) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / dyad axis / 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 H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of 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 / 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 / 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 speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDechassa, M.L. / Luger, K. / Chatterjee, N. / North, J.A. / Manohar, M. / Prasad, R. / Ottessen, J.J. / Poirier, M.G. / Bartholomew, B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088409 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM048413 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM083055 United States
CitationJournal: Mol.Cell.Biol. / Year: 2015
Title: Histone Acetylation near the Nucleosome Dyad Axis Enhances Nucleosome Disassembly by RSC and SWI/SNF.
Authors: Chatterjee, N. / North, J.A. / Dechassa, M.L. / Manohar, M. / Prasad, R. / Luger, K. / Ottesen, J.J. / Poirier, M.G. / Bartholomew, B.
History
DepositionFeb 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.country ..._citation.journal_id_CSD / _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Nov 6, 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 H3.2
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
I: DNA (147-MER)
J: DNA (147-MER)


Theoretical massNumber of molelcules
Total (without water)175,83810
Polymers175,83810
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55570 Å2
ΔGint-363 kcal/mol
Surface area73020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.400, 109.570, 180.810
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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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3.2


Mass: 11543.464 Da / Num. of mol.: 2 / Fragment: residues 39-136
Source method: isolated from a genetically manipulated source
Details: H3 acetylated at lysine 115 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#2: Protein Histone H4


Mass: 8910.394 Da / Num. of mol.: 2 / Fragment: residues 25-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A


Mass: 11724.677 Da / Num. of mol.: 2 / Fragment: residues 15-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 10376.928 Da / Num. of mol.: 2 / Fragment: residues 34-126
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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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (147-MER)


Mass: 45368.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#6: DNA chain DNA (147-MER)


Mass: 45359.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 1 types, 99 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: potassium chloride, potassium cacodylate, manganese chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→42.81 Å / Num. obs: 78406 / % possible obs: 95 % / Redundancy: 5.07 % / Rmerge(I) obs: 0.079 / Χ2: 0.97 / Net I/σ(I): 9.4 / Num. measured all: 405916 / Scaling rejects: 8119
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
2.4-2.495.30.4182.84370981581.1143499.9
2.49-2.595.380.3553.34417481371.0639199.9
2.59-2.75.30.2894.14414881581.09908100
2.7-2.855.50.234.9454538172146799.9
2.85-3.025.560.176.74602881800.9858199.9
3.02-3.265.480.1119.84539781470.974099.5
3.26-3.584.980.07214.53931777180.8389893.8
3.58-4.14.560.05916.93427372660.83112087.5
4.1-5.174.520.05220.53221169700.8272683.6
5.17-42.813.910.05220.13120675000.94185486.7

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Processing

Software
NameVersionClassification
CNSrefinement
d*TREK9.7Ldata reduction
d*TREKdata scaling
Cootmodel building
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P3L

1p3l


Resolution: 2.4→42.81 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2995 2804 1.8 %random
Rwork0.2559 140436 --
obs-74374 90.6 %-
Solvent computationBsol: 50.2668 Å2
Displacement parametersBiso max: 202.09 Å2 / Biso mean: 66.6097 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1-7.22 Å20 Å20 Å2
2---5.574 Å20 Å2
3----1.646 Å2
Refinement stepCycle: final / Resolution: 2.4→42.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5971 6021 99 0 12091
Biso mean--44.51 --
Num. residues----1046
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.017
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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