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- PDB-6kxv: Crystal structure of a nucleosome containing Leishmania histone H3 -

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Basic information

Entry
Database: PDB / ID: 6kxv
TitleCrystal structure of a nucleosome containing Leishmania histone H3
Components
  • DNA (146-MER)
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3
  • Histone H4
KeywordsDNA BINDING PROTEIN/DNA / Chromatin / Nucleosome / Leishmania / DNA BINDING PROTEIN-DNA complex
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 / 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 / nucleosomal DNA binding ...negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / 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 / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere organization / Meiotic synapsis / RNA Polymerase I Promoter Opening / 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 / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / innate immune response in mucosa / 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 / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / PKMTs methylate histone lysines / Meiotic recombination / Metalloprotease DUBs / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / antibacterial humoral response / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / protein-containing complex / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
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 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. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.63 Å
AuthorsDacher, M. / Taguchi, H. / Kujirai, T. / Kurumizaka, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP15F15729 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101076 Japan
Japan Society for the Promotion of ScienceJP25116002 Japan
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Incorporation and influence of Leishmania histone H3 in chromatin.
Authors: Dacher, M. / Tachiwana, H. / Horikoshi, N. / Kujirai, T. / Taguchi, H. / Kimura, H. / Kurumizaka, H.
History
DepositionSep 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H2A type 1-B/E
D: Histone H2B type 1-J
E: Histone H3
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
I: DNA (146-MER)
J: DNA (146-MER)


Theoretical massNumber of molelcules
Total (without water)200,77310
Polymers200,77310
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55760 Å2
ΔGint-422 kcal/mol
Surface area73110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.903, 101.101, 175.526
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain H and (resseq 35:85 or resseq 87:104 or resseq 106:119 or resseq 121:124))
21(chain D and (resseq 35:85 or resseq 87:104 or resseq 106:119 or resseq 121:124))
12(chain A and (resseq 34:108 or resseq 110:127))
22(chain E and (resseq 34:108 or resseq 110:127))
13(chain G and (resseq 15:70 or resseq 72:98 or resseq 100:117))
23(chain C and (resseq 15:70 or resseq 72:98 or resseq 100:117))
14(chain B and (resseq 25:26 or resseq 28:101))
24(chain F and (resseq 25:26 or resseq 28:101))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLULYSLYS(chain H and (resseq 35:85 or resseq 87:104 or resseq 106:119 or resseq 121:124))HH35 - 8539 - 89
121SERSERGLYGLY(chain H and (resseq 35:85 or resseq 87:104 or resseq 106:119 or resseq 121:124))HH87 - 10491 - 108
131LEULEUTHRTHR(chain H and (resseq 35:85 or resseq 87:104 or resseq 106:119 or resseq 121:124))HH106 - 119110 - 123
141TYRTYRALAALA(chain H and (resseq 35:85 or resseq 87:104 or resseq 106:119 or resseq 121:124))HH121 - 124125 - 128
211GLUGLULYSLYS(chain D and (resseq 35:85 or resseq 87:104 or resseq 106:119 or resseq 121:124))DD35 - 8539 - 89
221SERSERGLYGLY(chain D and (resseq 35:85 or resseq 87:104 or resseq 106:119 or resseq 121:124))DD87 - 10491 - 108
231LEULEUTHRTHR(chain D and (resseq 35:85 or resseq 87:104 or resseq 106:119 or resseq 121:124))DD106 - 119110 - 123
241TYRTYRALAALA(chain D and (resseq 35:85 or resseq 87:104 or resseq 106:119 or resseq 121:124))DD121 - 124125 - 128
112ARGARGALAALA(chain A and (resseq 34:108 or resseq 110:127))AA34 - 10838 - 112
122ARGARGGLUGLU(chain A and (resseq 34:108 or resseq 110:127))AA110 - 127114 - 131
212ARGARGALAALA(chain E and (resseq 34:108 or resseq 110:127))EE34 - 10838 - 112
222ARGARGGLUGLU(chain E and (resseq 34:108 or resseq 110:127))EE110 - 127114 - 131
113LYSLYSALAALA(chain G and (resseq 15:70 or resseq 72:98 or resseq 100:117))GG15 - 7019 - 74
123ASPASPGLYGLY(chain G and (resseq 15:70 or resseq 72:98 or resseq 100:117))GG72 - 9876 - 102
133VALVALPROPRO(chain G and (resseq 15:70 or resseq 72:98 or resseq 100:117))GG100 - 117104 - 121
213LYSLYSALAALA(chain C and (resseq 15:70 or resseq 72:98 or resseq 100:117))CC15 - 7019 - 74
223ASPASPGLYGLY(chain C and (resseq 15:70 or resseq 72:98 or resseq 100:117))CC72 - 9876 - 102
233VALVALPROPRO(chain C and (resseq 15:70 or resseq 72:98 or resseq 100:117))CC100 - 117104 - 121
114ASNASNILEILE(chain B and (resseq 25:26 or resseq 28:101))BB25 - 2629 - 30
124GLYGLYGLYGLY(chain B and (resseq 25:26 or resseq 28:101))BB28 - 10132 - 105
214ASNASNILEILE(chain F and (resseq 25:26 or resseq 28:101))FF25 - 2629 - 30
224GLYGLYGLYGLY(chain F and (resseq 25:26 or resseq 28:101))FF28 - 10132 - 105

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Histone H3 / Putative histone H3


Mass: 14990.575 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote)
Gene: LMJF_10_0870, LMJF_10_0990, LMJF_16_0570, LMJF_16_0575, LMJF_16_0610
Production host: Escherichia coli (E. coli) / References: UniProt: Q4QHB5
#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: 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: 14447.825 Da / Num. of mol.: 2
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: 14217.516 Da / Num. of mol.: 2
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
#5: DNA chain DNA (146-MER)


Mass: 45053.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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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: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium acetate, isopropanol, manganese chloride, trimethylamine N-oxide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.63→48.932 Å / Num. obs: 21054 / % possible obs: 99.6 % / Redundancy: 20.991 % / Biso Wilson estimate: 134.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.232 / Rrim(I) all: 0.238 / Χ2: 1.036 / Net I/σ(I): 10.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.63-3.8520.0032.2261.3465011332532500.5152.28497.7
3.85-4.1122.221.4532.4169881314631450.7531.487100
4.11-4.4421.9920.834.4564986295529550.9040.85100
4.44-4.8621.6640.5546.8558991272327230.9630.567100
4.86-5.4321.390.3969.3552811246924690.9810.405100
5.43-6.2520.6040.30911.1745432220522050.9860.317100
6.25-7.6318.6590.16817.3335172188518850.9950.173100
7.63-10.6621.4780.07836.1232131149614960.9990.08100
10.66-48.93218.9410.0647.92175399389260.9990.06198.7

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Processing

Software
NameVersionClassification
XSCALEBUILT=20170615data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
XDSBUILT=20170615data reduction
PHASER2.8.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AY8

5ay8


Resolution: 3.63→48.932 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.74
RfactorNum. reflection% reflection
Rfree0.2639 1080 5.13 %
Rwork0.2202 --
obs0.2225 21051 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 235.17 Å2 / Biso mean: 126.9751 Å2 / Biso min: 69.22 Å2
Refinement stepCycle: final / Resolution: 3.63→48.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5896 5980 0 0 11876
Num. residues----1042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312678
X-RAY DIFFRACTIONf_angle_d0.58318374
X-RAY DIFFRACTIONf_chiral_restr0.0342096
X-RAY DIFFRACTIONf_plane_restr0.0031312
X-RAY DIFFRACTIONf_dihedral_angle_d26.7176619
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11H772X-RAY DIFFRACTION6.258TORSIONAL
12D772X-RAY DIFFRACTION6.258TORSIONAL
21A914X-RAY DIFFRACTION6.258TORSIONAL
22E914X-RAY DIFFRACTION6.258TORSIONAL
31G926X-RAY DIFFRACTION6.258TORSIONAL
32C926X-RAY DIFFRACTION6.258TORSIONAL
41B722X-RAY DIFFRACTION6.258TORSIONAL
42F722X-RAY DIFFRACTION6.258TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.6294-3.79450.38341410.3264236797
3.7945-3.99450.32661520.31212447100
3.9945-4.24460.33311240.27312470100
4.2446-4.57220.28481330.24442475100
4.5722-5.03190.28061570.23142477100
5.0319-5.7590.29981210.23152508100
5.759-7.25190.25991220.2382560100
7.2519-48.9320.20461300.16312667100

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