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- PDB-6hkt: Structure of an H1-bound 6-nucleosome array -

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Basic information

Entry
Database: PDB / ID: 6hkt
TitleStructure of an H1-bound 6-nucleosome array
Components
  • (DNA (1122-MER)) x 2
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1
  • Histone H4
KeywordsDNA BINDING PROTEIN / chromatin / nucleosome array / chromatin fiber
Function / homology
Function and homology information


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 / Deposition of new CENPA-containing nucleosomes at the centromere ...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 / 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 / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / 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) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / 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 / 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 / UCH proteinases / 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 / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / 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 / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / protein-containing complex / extracellular space / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
: / 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 ...: / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / DNA (> 1000) / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 9.7 Å
AuthorsGarcia-Saez, I. / Dimitrov, S. / Petosa, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-10-LABX-0030, ANR-12-BSV5-0017, ANR-14-CE09-0019, ANR-16- CE12-0013, ANR-17-CE11-0019, ANR-18-CE12-0010 France
CitationJournal: Mol. Cell / Year: 2018
Title: Structure of an H1-Bound 6-Nucleosome Array Reveals an Untwisted Two-Start Chromatin Fiber Conformation.
Authors: Garcia-Saez, I. / Menoni, H. / Boopathi, R. / Shukla, M.S. / Soueidan, L. / Noirclerc-Savoye, M. / Le Roy, A. / Skoufias, D.A. / Bednar, J. / Hamiche, A. / Angelov, D. / Petosa, C. / Dimitrov, S.
History
DepositionSep 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 (1122-MER)
J: DNA (1122-MER)
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
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
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
U: Histone H3.1
V: Histone H4
W: Histone H2A type 1-B/E
X: Histone H2B type 1-J
Y: Histone H3.1
Z: Histone H4
0: Histone H2A type 1-B/E
1: Histone H2B type 1-J
u: Histone H3.1
v: Histone H4
w: Histone H2A type 1-B/E
x: Histone H2B type 1-J
y: Histone H3.1
z: Histone H4
2: Histone H2A type 1-B/E
3: Histone H2B type 1-J


Theoretical massNumber of molelcules
Total (without water)1,366,00550
Polymers1,366,00550
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area364070 Å2
ΔGint-2322 kcal/mol
Surface area509260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.078, 238.761, 674.368
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 4 types, 48 molecules AEaeKOkoUYuyBFbfLPlpVZvzCGcgMQ...

#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.: 12
Source method: isolated from a genetically manipulated source
Details: THE 3 N-TERMINAL RESIDUES (GSH) COME FROM THE EXPRESSION TAG
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 BL21(DE3) (bacteria) / References: UniProt: P68431
#2: Protein
Histone H4


Mass: 11676.703 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: THE 3 N-TERMINAL RESIDUES (GSH) COME FROM THE EXPRESSION TAG
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 BL21(DE3) (bacteria) / References: UniProt: P62805
#3: Protein
Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14447.825 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: THE 3 N-TERMINAL RESIDUES (GSH) COME FROM THE EXPRESSION TAG
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04908
#4: Protein
Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14217.516 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: THE 3 N-TERMINAL RESIDUES (GSH) COME FROM THE EXPRESSION TAG
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P06899

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (1122-MER)


Mass: 344755.281 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Six tandem 187-bp repeats containing Widom 601 sequence
Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (1122-MER)


Mass: 348512.312 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Six tandem 187-bp repeats containing Widom 601 sequence
Source: (synth.) synthetic construct (others)

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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: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 15% MPD, 0.1 M NaCl and 0.1 M Tris pH 8.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.99187 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 9.7→49.1 Å / Num. obs: 11252 / % possible obs: 99.2 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.09 / Rrim(I) all: 0.23 / Net I/σ(I): 7
Reflection shellResolution: 9.7→10.85 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3152 / CC1/2: 0.604 / Rpim(I) all: 0.362 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LZ0

3lz0


Resolution: 9.7→49.074 Å / SU ML: 1.68 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 34.02
RfactorNum. reflection% reflection
Rfree0.286 572 5.05 %
Rwork0.2537 --
obs0.2554 11204 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 9.7→49.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36120 46002 0 0 82122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00488210
X-RAY DIFFRACTIONf_angle_d0.726128842
X-RAY DIFFRACTIONf_dihedral_angle_d31.61936678
X-RAY DIFFRACTIONf_chiral_restr0.05914628
X-RAY DIFFRACTIONf_plane_restr0.0038520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
9.7004-10.20750.4188790.36941508X-RAY DIFFRACTION100
10.2075-10.84060.3256790.31681467X-RAY DIFFRACTION100
10.8406-11.66720.3387800.26711487X-RAY DIFFRACTION100
11.6672-12.82230.2957820.23121499X-RAY DIFFRACTION100
12.8223-14.63450.2751860.23761516X-RAY DIFFRACTION100
14.6345-18.27810.2806700.29251561X-RAY DIFFRACTION100
18.2781-49.0750.234960.20171594X-RAY DIFFRACTION99

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