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- PDB-8yti: Crystal Structure of Nucleosome-H1x Linker Histone Assembly (stic... -

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Entry
Database: PDB / ID: 8yti
TitleCrystal Structure of Nucleosome-H1x Linker Histone Assembly (sticky-169a DNA fragment)
Components
  • (DNA (169-MER)) x 2
  • Histone H1x
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1
  • Histone H4
KeywordsDNA BINDING PROTEIN/DNA / linker histone / nucleosome binding / chromatin structure / chromatin compaction / histone variants / STRUCTURAL PROTEIN-DNA complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of DNA recombination / chromosome condensation / nucleosomal DNA binding / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / 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 ...negative regulation of DNA recombination / chromosome condensation / nucleosomal DNA binding / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / 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 / UCH proteinases / nucleosome / heterochromatin formation / E3 ubiquitin ligases ubiquitinate target proteins / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromosome / Factors involved in megakaryocyte development and platelet production / 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) / double-stranded DNA binding / defense response to Gram-negative bacterium / Oxidative Stress Induced Senescence / 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 / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / nucleolus / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site ...Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / : / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1 / Histone H1.10
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAdhireksan, Z. / Qiuye, B. / Padavattan, S. / Davey, C.A.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: To Be Published
Title: Linker Histones Associate Heterogeneously with Nucleosomes in the Condensed State
Authors: Adhireksan, Z. / Sharma, D. / Qiuye, B. / Lee, P.L. / Padavattan, S. / Davey, C.A.
History
DepositionMar 26, 2024Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 3, 2024ID: 7XX7
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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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 type 1-B/E
D: Histone H2B type 1-J
E: Histone H3.1
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
I: DNA (169-MER)
J: DNA (169-MER)
K: Histone H3.1
L: Histone H4
M: Histone H2A type 1-B/E
N: Histone H2B type 1-J
O: Histone H3.1
P: Histone H4
Q: Histone H2A type 1-B/E
R: Histone H2B type 1-J
S: DNA (169-MER)
T: DNA (169-MER)
U: Histone H1x
V: Histone H1x
hetero molecules


Theoretical massNumber of molelcules
Total (without water)476,17290
Polymers473,49122
Non-polymers2,68068
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.852, 102.111, 216.179
Angle α, β, γ (deg.)90.000, 96.337, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 5 types, 18 molecules AEKOBFLPCGMQDHNRUV

#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: 15437.167 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#2: Protein
Histone H4


Mass: 11394.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein
Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14165.551 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#4: Protein
Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 13935.239 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli (E. coli) / References: UniProt: P06899
#7: Protein Histone H1x


Mass: 22543.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H1FX / Production host: Escherichia coli (E. coli) / References: UniProt: Q92522

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DNA chain , 2 types, 4 molecules ISJT

#5: DNA chain DNA (169-MER)


Mass: 52173.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (169-MER)


Mass: 52164.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 225 molecules

#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#9: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 52 / Source method: obtained synthetically / Formula: Ca
#10: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 40-45 mM CaCl2, 25 mM KCl, 10 mM Na-acetate (pH 4.5)

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Data collection

DiffractionMean temperature: 98 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→92.22 Å / Num. obs: 124272 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.998 / Net I/σ(I): 9.8
Reflection shellResolution: 2.7→2.85 Å / Num. unique obs: 17749 / CC1/2: 0.521

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→92.22 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 18.389 / SU ML: 0.347 / Cross valid method: FREE R-VALUE / ESU R: 0.98 / ESU R Free: 0.349
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2669 2402 1.933 %
Rwork0.2096 121849 -
all0.211 --
obs-124251 99.562 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 88.021 Å2
Baniso -1Baniso -2Baniso -3
1--2.576 Å2-0 Å20.622 Å2
2---1.286 Å20 Å2
3---3.634 Å2
Refinement stepCycle: LAST / Resolution: 2.7→92.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14012 13846 68 157 28083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01229724
X-RAY DIFFRACTIONr_bond_other_d0.0010.01821966
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.39142984
X-RAY DIFFRACTIONr_angle_other_deg1.3342.08751100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59851745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.68418.633812
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.796152795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.47915195
X-RAY DIFFRACTIONr_chiral_restr0.0660.23870
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0223817
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026626
X-RAY DIFFRACTIONr_nbd_refined0.1860.25625
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.222503
X-RAY DIFFRACTIONr_nbtor_refined0.2040.212507
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.211127
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2612
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0690.233
X-RAY DIFFRACTIONr_metal_ion_refined0.2030.215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2850.252
X-RAY DIFFRACTIONr_nbd_other0.2710.2196
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2330.217
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1520.22
X-RAY DIFFRACTIONr_mcbond_it4.1927.477034
X-RAY DIFFRACTIONr_mcbond_other4.1917.477033
X-RAY DIFFRACTIONr_mcangle_it6.4811.1838761
X-RAY DIFFRACTIONr_mcangle_other6.4811.1848762
X-RAY DIFFRACTIONr_scbond_it4.92910.30422690
X-RAY DIFFRACTIONr_scbond_other4.92910.30422691
X-RAY DIFFRACTIONr_scangle_it7.63715.46834223
X-RAY DIFFRACTIONr_scangle_other7.63715.46834224
X-RAY DIFFRACTIONr_lrange_it10.57399.62437800
X-RAY DIFFRACTIONr_lrange_other10.56799.61837786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.41770.3778759X-RAY DIFFRACTION97.4057
2.77-2.8460.391870.3548619X-RAY DIFFRACTION98.3032
2.846-2.9290.3842060.3298387X-RAY DIFFRACTION98.6001
2.929-3.0190.3452060.3018216X-RAY DIFFRACTION99.7631
3.019-3.1180.2981810.2698024X-RAY DIFFRACTION100
3.118-3.2270.3051450.2577766X-RAY DIFFRACTION99.9874
3.227-3.3490.2611420.2367498X-RAY DIFFRACTION99.9738
3.349-3.4860.281390.2237284X-RAY DIFFRACTION100
3.486-3.640.2771230.2116961X-RAY DIFFRACTION99.9859
3.64-3.8180.255800.2056660X-RAY DIFFRACTION100
3.818-4.0250.2591200.1976336X-RAY DIFFRACTION100
4.025-4.2690.2511090.1915999X-RAY DIFFRACTION100
4.269-4.5630.2591120.1745630X-RAY DIFFRACTION100
4.563-4.9290.23860.1855244X-RAY DIFFRACTION99.9812
4.929-5.3990.252910.1884867X-RAY DIFFRACTION100
5.399-6.0350.258850.1914373X-RAY DIFFRACTION99.9776
6.035-6.9680.258830.1873901X-RAY DIFFRACTION100
6.968-8.5320.199720.1663287X-RAY DIFFRACTION100
8.532-12.0570.207370.1442573X-RAY DIFFRACTION100
12.057-92.220.18210.1861465X-RAY DIFFRACTION99.4645

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