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Basic information

Entry
Database: PDB / ID: 5z23
TitleCrystal structure of the nucleosome containing a chimeric histone H3/CENP-A CATD
Components
  • DNA (146-MER)
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1,Histone H3-like centromeric protein A,Histone H3.1
  • Histone H4
KeywordsDNA BINDING PROTEIN/DNA / Nucleosome / Chromosome / CENP-A / centromere / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


CENP-A containing chromatin assembly / kinetochore assembly / protein localization to chromosome, centromeric region / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin ...CENP-A containing chromatin assembly / kinetochore assembly / protein localization to chromosome, centromeric region / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / pericentric heterochromatin / 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 / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / 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 / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / 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 / Resolution of Sister Chromatid Cohesion / 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 / RHO GTPases Activate Formins / 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 / Separation of Sister Chromatids / 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 / 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) / 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 / chromatin binding / protein-containing complex / DNA binding / extracellular space / RNA binding
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, 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H3-like centromeric protein A / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.73 Å
AuthorsArimura, Y. / Tachiwana, H. / Takagi, H.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP25116002 Japan
Japan Society for the Promotion of ScienceJP17K15043 Japan
Japan Society for the Promotion of ScienceJP17H01408 Japan
Japan Science and TechnologyJPMJCR16G1 Japan
Japan Agency for Medical Research and DevelopmentPlatform Project for Supporting in Drug Discovery and Life Science Research Japan
CitationJournal: Nat Commun / Year: 2019
Title: The CENP-A centromere targeting domain facilitates H4K20 monomethylation in the nucleosome by structural polymorphism.
Authors: Arimura, Y. / Tachiwana, H. / Takagi, H. / Hori, T. / Kimura, H. / Fukagawa, T. / Kurumizaka, H.
History
DepositionDec 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.1,Histone H3-like centromeric protein A,Histone H3.1
B: Histone H4
C: Histone H2A type 1-B/E
D: Histone H2B type 1-J
E: Histone H3.1,Histone H3-like centromeric protein A,Histone H3.1
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)211,11910
Polymers211,11910
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55270 Å2
ΔGint-394 kcal/mol
Surface area73120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.641, 100.745, 173.431
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
11chain A
21(chain E and resid 38 through 136)
12chain I
22chain J
13chain B
23(chain F and resid 23 through 100)
14(chain C and resid 15 through 117)
24(chain G and resid 15 through 117)
15(chain D and resid 33 through 123)
25(chain H and resid 33 through 123)

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROARGARGchain AAA38 - 13642 - 140
21PROPROARGARG(chain E and resid 38 through 136)EE38 - 13642 - 140
12DADADTDTchain III1 - 1461 - 146
22DADADTDTchain JJJ147 - 2921 - 146
13ARGARGPHEPHEchain BBB23 - 10027 - 104
23ARGARGPHEPHE(chain F and resid 23 through 100)FF23 - 10027 - 104
14LYSLYSPROPRO(chain C and resid 15 through 117)CC15 - 11719 - 121
24LYSLYSPROPRO(chain G and resid 15 through 117)GG15 - 11719 - 121
15ARGARGSERSER(chain D and resid 33 through 123)DD33 - 12337 - 127
25ARGARGSERSER(chain H and resid 33 through 123)HH33 - 12337 - 127

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein Histone H3.1,Histone H3-like centromeric protein A,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 / Centromere autoantigen A / Centromere protein A / CENP-A


Mass: 16063.921 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Chimera protein H3CATD, in which amino acid residues 76-113 of human histone H3.1 were replaced by corresponding amino acid residues 75-114 of human CENP-A.
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, CENPA
Plasmid: pH3CATD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P68431, UniProt: P49450
#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
Plasmid: pH4 / Details (production host): pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P62805
#3: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 18406.734 Da / Num. of mol.: 2 / Mutation: L51M,L58M,L93M
Source method: isolated from a genetically manipulated source
Details: selenomethionine (Se-Met)-substituted H2A, the codons for H2A Leu51, Leu58, and Leu93 were replaced by the methionine codon
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Plasmid: pH2A / Details (production host): pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P04908
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14358.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Se-Met-substituted H2B / Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Plasmid: pH2B / Details (production host): pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / 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) / Strain (production host): DH5a
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: potassium cacodylate, potassium chloride, manganese chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.71→50 Å / Num. obs: 45350 / % possible obs: 96.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 65.32 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Χ2: 1.002 / Net I/σ(I): 15 / Num. measured all: 258570
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.71-2.814.80.49241800.7970.2330.5460.94190.3
2.81-2.924.80.37341840.8750.1740.414190.3
2.92-3.054.90.27942530.9430.1290.3091.06192.1
3.05-3.215.10.17944210.9790.0810.1971.08994.9
3.21-3.415.30.12145800.9910.0540.1330.99698.5
3.41-3.685.60.09246630.9940.0410.1010.95899.8
3.68-4.0560.0746740.9960.030.0770.94699.9
4.05-4.636.50.05647120.9980.0230.0610.99299.8
4.63-5.846.80.07447670.9960.030.0790.98299.9
5.84-506.70.04849160.9980.020.0531.06299

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å50.14 Å
Translation4 Å50.14 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AFA

3afa


Resolution: 2.73→47.884 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2614 1985 4.38 %
Rwork0.2029 43299 -
obs0.2055 45284 96.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.53 Å2 / Biso mean: 82.9725 Å2 / Biso min: 23.39 Å2
Refinement stepCycle: final / Resolution: 2.73→47.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6028 5980 0 0 12008
Num. residues----1047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112824
X-RAY DIFFRACTIONf_angle_d1.20818572
X-RAY DIFFRACTIONf_chiral_restr0.0582105
X-RAY DIFFRACTIONf_plane_restr0.0081337
X-RAY DIFFRACTIONf_dihedral_angle_d25.0896691
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A972X-RAY DIFFRACTION12.778TORSIONAL
12E972X-RAY DIFFRACTION12.778TORSIONAL
21I2912X-RAY DIFFRACTION12.778TORSIONAL
22J2912X-RAY DIFFRACTION12.778TORSIONAL
31B754X-RAY DIFFRACTION12.778TORSIONAL
32F754X-RAY DIFFRACTION12.778TORSIONAL
41C882X-RAY DIFFRACTION12.778TORSIONAL
42G882X-RAY DIFFRACTION12.778TORSIONAL
51D806X-RAY DIFFRACTION12.778TORSIONAL
52H806X-RAY DIFFRACTION12.778TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7301-2.79830.35881180.28532658277684
2.7983-2.8740.34111280.25932872300091
2.874-2.95850.31651290.24982896302591
2.9585-3.0540.33911320.24712906303892
3.054-3.16310.30421390.26012988312794
3.1631-3.28980.34421440.23363092323697
3.2898-3.43940.27741470.22633160330799
3.4394-3.62070.28851480.209931813329100
3.6207-3.84750.27781480.205832143362100
3.8475-4.14440.23411480.187931943342100
4.1444-4.56120.22811490.183932473396100
4.5612-5.22050.2511500.186832263376100
5.2205-6.57460.29521470.21832833430100
6.5746-47.89130.20021580.1653382354099

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