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- PDB-1eqz: X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1eqz
TitleX-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION
Components
  • (PROTEIN (HISTONE ...) x 4
  • 146 NUCLEOTIDES LONG DNA
KeywordsSTRUCTURAL PROTEIN/DNA / NUCLEOSOME / NUCLEOSOME CORE PARTICLE / HISTONE / MICROGRAVITY HISTONE OCTAMER / DNA PALINDROME / DNA PROTEIN COMPLEX / CHROMATIN / CHROMOSOMAL PROTEIN / HISTONE FOLD / BENT DNA / STRUCTURAL PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


PKMTs methylate histone lysines / HDMs demethylate histones / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Processing of DNA double-strand break ends / Interleukin-7 signaling / Chromatin modifying enzymes ...PKMTs methylate histone lysines / HDMs demethylate histones / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Processing of DNA double-strand break ends / Interleukin-7 signaling / Chromatin modifying enzymes / Metalloprotease DUBs / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / Oxidative Stress Induced Senescence / HDACs deacetylate histones / HATs acetylate histones / Transcriptional regulation by small RNAs / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / 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 / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Regulation of endogenous retroelements by KRAB-ZFP proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / UCH proteinases / B-WICH complex positively regulates rRNA expression / Ub-specific processing proteases / Deposition of new CENPA-containing nucleosomes at the centromere / Factors involved in megakaryocyte development and platelet production / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / protein heterodimerization activity / protein-containing complex binding / 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
CACODYLATE ION / : / : / DNA / DNA (> 10) / DNA (> 100) / Histone H2A-IV / Histone H2B 5 / Histone H2B 7 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR, molecular replacement / Resolution: 2.5 Å
AuthorsHanson, B.L. / Harp, J.M. / Timm, D.E. / Bunick, G.J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Asymmetries in the nucleosome core particle at 2.5 A resolution.
Authors: Harp, J.M. / Hanson, B.L. / Timm, D.E. / Bunick, G.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: X-Ray Diffraction Analysis of Crystals Containing Two Fold Symmetric Nucleosome Core Particles
Authors: Harp, J.M. / Uberbacher, E.C. / Roberson, A. / Palmer, E. / Gewiess, A. / Bunick, G.J.
#2: Journal: Thesis / Year: 1985
Title: Structural Analysis of Members of a Repeated DNA Family in Primates
Authors: Hauser, L.J.
History
DepositionApr 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: 146 NUCLEOTIDES LONG DNA
J: 146 NUCLEOTIDES LONG DNA
A: PROTEIN (HISTONE H2A)
B: PROTEIN (HISTONE H2B)
C: PROTEIN (HISTONE H3)
D: PROTEIN (HISTONE H4)
E: PROTEIN (HISTONE H2A)
F: PROTEIN (HISTONE H2B)
G: PROTEIN (HISTONE H3)
H: PROTEIN (HISTONE H4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,89235
Polymers199,58610
Non-polymers1,30625
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.280, 109.710, 181.120
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 146 NUCLEOTIDES LONG DNA


Mass: 45054.844 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: 146 BP DNA PALINDROME BASED ON 5' HALF OF NUCLEOSOME PHASING SEQUENCE OF ALPHA SATELLITE DNA FROM HUMAN X CHROMOSOME BAM H1 REPEAT

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PROTEIN (HISTONE ... , 4 types, 8 molecules AEBFCGDH

#2: Protein PROTEIN (HISTONE H2A)


Mass: 13969.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER / Source: (natural) Gallus gallus (chicken) / Organelle: ERYTHROCYTE NUCLEUS / Tissue: BLOOD / References: UniProt: P02263
#3: Protein PROTEIN (HISTONE H2B)


Mass: 13953.251 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER / Source: (natural) Gallus gallus (chicken) / Organelle: ERYTHROCYTE NUCLEUS / Tissue: BLOOD / References: UniProt: P02279, UniProt: P0C1H5*PLUS
#4: Protein PROTEIN (HISTONE H3)


Mass: 15421.101 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER / Source: (natural) Gallus gallus (chicken) / Organelle: ERYTHROCYTE NUCLEUS / Tissue: BLOOD / References: UniProt: P84229
#5: Protein PROTEIN (HISTONE H4)


Mass: 11394.426 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER / Source: (natural) Gallus gallus (chicken) / Organelle: ERYTHROCYTE NUCLEUS / Tissue: BLOOD / References: UniProt: P62801

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Non-polymers , 5 types, 374 molecules

#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Mn
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 53.06 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6 / Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mM11KCl
210 mMpotassium cacodylate11
31 mMPMSF11
550 mM12KCl
610 mMpotassium cacodylate12
71 mMPMSF12
411MnCl2high concentration
812MnCl2low concentration

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.003
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 18, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003 Å / Relative weight: 1
ReflectionResolution: 2.5→25.4 Å / Num. all: 73319 / Num. obs: 73319 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 42.7 Å2 / Rsym value: 0.053
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 72200 / Num. measured all: 605950 / Rmerge(I) obs: 0.045

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Processing

Software
NameClassification
SCALEPACKdata scaling
CCP4model building
CNSrefinement
CCP4phasing
CNSphasing
RefinementMethod to determine structure: SIR, molecular replacement
Starting model: 2HIO, 1AOI

2hio

1aoi


Resolution: 2.5→25.34 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2059998.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.282 7303 10.1 %RANDOM
Rwork0.219 ---
obs0.219 72200 98.6 %-
all-72200 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.68 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso mean: 53.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.98 Å20 Å20 Å2
2---5.53 Å20 Å2
3----0.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-25.4 Å
Luzzati sigma a0.29 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.5→25.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6906 5988 29 349 13272
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.33
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.641.5
X-RAY DIFFRACTIONc_mcangle_it4.962
X-RAY DIFFRACTIONc_scbond_it4.682
X-RAY DIFFRACTIONc_scangle_it5.982.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PADNA-RNA.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.33

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