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- PDB-1f66: 2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING ... -

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Basic information

Entry
Database: PDB / ID: 1f66
Title2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z
Components
  • HISTONE H2A.Z
  • HISTONE H2B
  • HISTONE H3
  • HISTONE H4
  • PALINDROMIC 146 BASE PAIR DNA FRAGMENT
KeywordsSTRUCTURAL PROTEIN/DNA / NUCLEOSOME / CHROMATIN / HISTONE / HISTONE VARIANT / PROTEIN DNA INTERACTION / NUCLEOPROTEIN / SUPERCOILED DNA / COMPLEX (NUCLEOSOME CORE-DNA) / STRUCTURAL PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


SUMOylation of chromatin organization proteins / Deposition of new CENPA-containing nucleosomes at the centromere / heterochromatin formation => GO:0031507 / Condensation of Prophase Chromosomes / G2/M DNA damage checkpoint / HDMs demethylate histones / Processing of DNA double-strand break ends / Nonhomologous End-Joining (NHEJ) / PRC2 methylates histones and DNA / HATs acetylate histones ...SUMOylation of chromatin organization proteins / Deposition of new CENPA-containing nucleosomes at the centromere / heterochromatin formation => GO:0031507 / Condensation of Prophase Chromosomes / G2/M DNA damage checkpoint / HDMs demethylate histones / Processing of DNA double-strand break ends / Nonhomologous End-Joining (NHEJ) / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Estrogen-dependent gene expression / nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / heterochromatin / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / cellular response to estradiol stimulus / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / euchromatin / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / chromatin DNA binding / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / 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 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 / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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.Z / Histone H2A.Z / Histone H4 / Histone H3.2 / :
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Mus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsSuto, R.K. / Clarkson, M.J. / Tremethick, D.J. / Luger, K.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structure of a nucleosome core particle containing the variant histone H2A.Z.
Authors: Suto, R.K. / Clarkson, M.J. / Tremethick, D.J. / Luger, K.
History
DepositionJun 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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 BASE PAIR DNA FRAGMENT
J: PALINDROMIC 146 BASE PAIR DNA FRAGMENT
A: HISTONE H3
B: HISTONE H4
C: HISTONE H2A.Z
D: HISTONE H2B
E: HISTONE H3
F: HISTONE H4
G: HISTONE H2A.Z
H: HISTONE H2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,85925
Polymers199,03510
Non-polymers82415
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.660, 183.207, 109.922
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 BASE PAIR DNA FRAGMENT


Mass: 45054.844 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein , 4 types, 8 molecules AEBFCGDH

#2: Protein HISTONE H3 /


Mass: 15507.190 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) / References: UniProt: Q7ZT64, UniProt: P84233*PLUS
#3: Protein HISTONE H4 /


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P62806
#4: Protein HISTONE H2A.Z /


Mass: 13581.796 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) / References: UniProt: P17317, UniProt: P0C0S5*PLUS
#5: Protein HISTONE H2B /


Mass: 13979.291 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) / References: UniProt: P02281

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Non-polymers , 2 types, 340 molecules

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


Mass: 54.938 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6353.21
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2921vapor diffusion, sitting drop6MnCl2, KCl, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
2922vapor diffusion, sitting drop6MnCl2, KCl, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
2923vapor diffusion, sitting drop6MnCl2, KCl, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1MnCl211
2KCl11
3cacodylateCacodylic acid11
4KCl12
Crystal grow
*PLUS
Method: vapor diffusion / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
180-96 mM1dropMnCl2
268-78 mM1dropKCl
320 mMpotassium cacodylate1drop
44 mg/mlprotein1drop
540-48 mM1reservoirMnCl2
634-39 mM1reservoirKCl
720 mMpotassium cacodylate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONALS 5.0.211.1
SYNCHROTRONALS 5.0.221.1
SYNCHROTRONALS 5.0.231
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDOct 29, 1999
ADSC QUANTUM 42CCDOct 29, 1999
ADSC QUANTUM 43CCDOct 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
211
ReflectionResolution: 2.6→25 Å / Num. all: 66416 / Num. obs: 65959 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 7.7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3 % / Rmerge(I) obs: 0.245 / Num. unique all: 3292 / % possible all: 99.9
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.6→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 2011 3.1 %RANDOM
Rwork0.1925 ---
all-65959 --
obs-63948 99.6 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.868 Å20 Å20 Å2
2---4.004 Å20 Å2
3---9.873 Å2
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6079 5980 15 325 12399
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.013
X-RAY DIFFRACTIONc_angle_deg1.555
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 25 Å / % reflection Rfree: 3.1 % / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.55

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