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- PDB-3wa9: The nucleosome containing human H2A.Z.1 -

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Basic information

Entry
Database: PDB / ID: 3wa9
TitleThe nucleosome containing human H2A.Z.1
Components
  • DNA (146-MER)
  • Histone H2A.Z
  • Histone H2B type 1-J
  • Histone H3.1
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / histone fold / DNA binding / nucleus / chromatin formation / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


nucleosomal DNA binding / negative regulation of tumor necrosis factor-mediated signaling pathway / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / heterochromatin / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends ...nucleosomal DNA binding / negative regulation of tumor necrosis factor-mediated signaling pathway / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / heterochromatin / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / 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 / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / lipopolysaccharide binding / RNA Polymerase I Promoter Escape / cellular response to estradiol stimulus / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / euchromatin / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / chromatin DNA binding / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / antibacterial humoral response / nucleosome / heterochromatin formation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / gene expression / killing of cells of another organism / Estrogen-dependent gene expression / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / cadherin binding / 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 / extracellular space / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol
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 type 1-J / Histone H2A.Z / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsHorikoshi, N. / Sato, K. / Shimada, K. / Arimura, Y. / Osakabe, A. / Tachiwana, H. / Iwasaki, W. / Kagawa, W. / Harata, M. / Kimura, H. / Kurumizaka, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2
Authors: Horikoshi, N. / Sato, K. / Shimada, K. / Arimura, Y. / Osakabe, A. / Tachiwana, H. / Hayashi-Takanaka, Y. / Iwasaki, W. / Kagawa, W. / Harata, M. / Kimura, H. / Kurumizaka, H.
History
DepositionApr 30, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
A: Histone H3.1
B: Histone H4
C: Histone H2A.Z
D: Histone H2B type 1-J
E: Histone H3.1
F: Histone H4
G: Histone H2A.Z
H: Histone H2B type 1-J
I: DNA (146-MER)
J: DNA (146-MER)


Theoretical massNumber of molelcules
Total (without water)201,06310
Polymers201,06310
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55620 Å2
ΔGint-388 kcal/mol
Surface area72230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.903, 109.390, 181.764
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 15719.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3.1 / Plasmid: pHCE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P68431
#2: Protein Histone H4


Mass: 11676.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H4 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P62805
#3: Protein Histone H2A.Z / H2A/z


Mass: 13864.073 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2A.Z.1 / Plasmid: pHCE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0C0S5
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14217.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2B / Plasmid: pHCE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06899
#5: DNA chain DNA (146-MER)


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

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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: 2.59 Å3/Da / Density % sol: 52.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 22, 2010
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.07→50 Å / Num. all: 40613 / Num. obs: 40504 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 63.06 Å2 / Rsym value: 0.079 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
3.07-3.185.94.540170.4891100
3.18-3.3166.839920.33199.9
3.31-3.4669.640010.2321100
3.46-3.646.114.140040.1581100
3.64-3.876.218.439990.1211100
3.87-4.176.424.740350.0881100
4.17-4.596.533.740580.0651100
4.59-5.256.638.240630.0561100
5.25-6.616.640.641270.0521100
6.61-506.362.742080.031198

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AFA

3afa


Resolution: 3.07→38.963 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8168 / SU ML: 0.36 / σ(F): 1.34 / Phase error: 25.19 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2707 1994 5.02 %RANDOM
Rwork0.2224 ---
all0.2707 39714 --
obs0.2248 39710 99.81 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.734 Å2 / ksol: 0.276 e/Å3
Displacement parametersBiso max: 168.33 Å2 / Biso mean: 73.5777 Å2 / Biso min: 17.26 Å2
Baniso -1Baniso -2Baniso -3
1-6.4237 Å2-0 Å20 Å2
2---11.4426 Å20 Å2
3---5.0189 Å2
Refinement stepCycle: LAST / Resolution: 3.07→38.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5945 5980 0 0 11925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812729
X-RAY DIFFRACTIONf_angle_d1.31518435
X-RAY DIFFRACTIONf_chiral_restr0.0652099
X-RAY DIFFRACTIONf_plane_restr0.0051314
X-RAY DIFFRACTIONf_dihedral_angle_d27.065232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
3.07-3.14680.34781570.3006263527922635100
3.1468-3.23180.32151480.2731265328012653100
3.2318-3.32680.31691520.2542264127932641100
3.3268-3.43420.30021400.2445267628162676100
3.4342-3.55680.30331180.2309267227902672100
3.5568-3.69910.26181520.22267028222670100
3.6991-3.86730.28251350.221268428192684100
3.8673-4.0710.23431290.2173268928182689100
4.071-4.32580.26581520.1991269128432691100
4.3258-4.65930.23811450.2062268428292684100
4.6593-5.12720.29321360.21270928452709100
5.1272-5.8670.27151380.23273928772739100
5.867-7.38350.29981440.2372275228962752100
7.3835-38.96560.21911480.197828212969282198

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