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- PDB-4z5t: The nucleosome containing human H3.5 -

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Basic information

Entry
Database: PDB / ID: 4z5t
TitleThe nucleosome containing human H3.5
Components
  • DNA (146-MER)
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.3C
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / histone fold / DNA binding / nucleus / spermatogenesis / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


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 / 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 / telomere organization / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / innate immune response in mucosa / 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 / euchromatin / 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 / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / Meiotic recombination / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RMTs methylate histone arginines / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / UCH proteinases / antibacterial humoral response / heterochromatin formation / nucleosome / 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 / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Processing of DNA double-strand break ends / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / killing of cells of another organism / Estrogen-dependent gene expression / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / 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, 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 H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.3C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsUrahama, T. / Harada, A. / Maehara, K. / Horikoshi, N. / Sato, K. / Sato, Y. / Shiraishi, K. / Sugino, N. / Osakabe, A. / Tachiwana, H. ...Urahama, T. / Harada, A. / Maehara, K. / Horikoshi, N. / Sato, K. / Sato, Y. / Shiraishi, K. / Sugino, N. / Osakabe, A. / Tachiwana, H. / Kagawa, W. / Kimura, H. / Ohkawa, Y. / Kurumizaka, H.
Funding support Japan, 4items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology25116002 Japan
Ministry of Education, Culture, Sports, Science and Technology25116005 Japan
Ministry of Education, Culture, Sports, Science and Technology25131706 Japan
Ministry of Education, Culture, Sports, Science and Technology26116521 Japan
CitationJournal: Epigenetics Chromatin / Year: 2016
Title: Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis.
Authors: Urahama, T. / Harada, A. / Maehara, K. / Horikoshi, N. / Sato, K. / Sato, Y. / Shiraishi, K. / Sugino, N. / Osakabe, A. / Tachiwana, H. / Kagawa, W. / Kimura, H. / Ohkawa, Y. / Kurumizaka, H.
History
DepositionApr 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 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_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

Downloads & links

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Assembly

Deposited unit
A: Histone H3.3C
B: Histone H4
C: Histone H2A type 1-B/E
D: Histone H2B type 1-J
E: Histone H3.3C
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)201,84610
Polymers201,84610
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55000 Å2
ΔGint-404 kcal/mol
Surface area72690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.891, 109.129, 174.492
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
21chain E
12chain B
22chain F
13chain C
23chain G
14chain D
24chain H
15chain I
25chain J

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 AAA37 - 13341 - 137
21HISHISARGARGchain EEE38 - 13342 - 137
12LYSLYSGLYGLYchain BBB20 - 10224 - 106
22ASPASPGLYGLYchain FFF24 - 10228 - 106
13ALAALALYSLYSchain CCC14 - 11818 - 122
23LYSLYSLYSLYSchain GGG15 - 11819 - 122
14ARGARGALAALAchain DDD33 - 12437 - 128
24ARGARGALAALAchain HHH33 - 12437 - 128
15DADADTDTchain III1 - 1461 - 146
25DADADTDTchain JJJ147 - 2921 - 146

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein Histone H3.3C / Histone H3.5


Mass: 15527.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3F3C / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6NXT2
#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: 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: 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 / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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 / Plasmid: pUC19 / 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: 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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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 MX225HE / Detector: CCD / Date: Jul 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 50581 / % possible obs: 99.5 % / Redundancy: 8.8 % / Biso Wilson estimate: 62.74 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.032 / Rrim(I) all: 0.1 / Χ2: 1.788 / Net I/av σ(I): 28.208 / Net I/σ(I): 10.2 / Num. measured all: 447587
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.96.40.548240.7220.2070.5430.80996.5
2.9-3.027.10.43450080.8520.1720.4680.88499.9
3.02-3.157.50.33749960.9540.130.3621.01899.9
3.15-3.3280.27950440.970.1030.2981.137100
3.32-3.538.70.20550420.9890.0720.2181.349100
3.53-3.89.40.14450450.9950.0490.1531.539100
3.8-4.1810.10.10550580.9970.0340.111.655100
4.18-4.7910.70.07851130.9980.0250.0821.93100
4.79-6.0310.30.08651390.9970.0280.092.97399.9
6.03-5010.20.05453120.9980.0180.0573.2598.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AV2

3av2


Resolution: 2.8→37.812 Å / SU ML: 0.46 / Cross valid method: NONE / σ(F): 1.43 / Phase error: 31.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2694 2538 5.08 %Random selection
Rwork0.2277 47386 --
obs0.2298 49924 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 270.06 Å2 / Biso mean: 99.6349 Å2 / Biso min: 17.48 Å2
Refinement stepCycle: final / Resolution: 2.8→37.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5919 5980 0 0 11899
Num. residues----1040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512704
X-RAY DIFFRACTIONf_angle_d0.81518414
X-RAY DIFFRACTIONf_chiral_restr0.0342096
X-RAY DIFFRACTIONf_plane_restr0.0041323
X-RAY DIFFRACTIONf_dihedral_angle_d29.3795235
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A916X-RAY DIFFRACTION9.828TORSIONAL
12E916X-RAY DIFFRACTION9.828TORSIONAL
21B748X-RAY DIFFRACTION9.828TORSIONAL
22F748X-RAY DIFFRACTION9.828TORSIONAL
31C940X-RAY DIFFRACTION9.828TORSIONAL
32G940X-RAY DIFFRACTION9.828TORSIONAL
41D820X-RAY DIFFRACTION9.828TORSIONAL
42H820X-RAY DIFFRACTION9.828TORSIONAL
51I2912X-RAY DIFFRACTION9.828TORSIONAL
52J2912X-RAY DIFFRACTION9.828TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.85390.46331520.405725972749100
2.8539-2.91210.42441500.376725812731100
2.9121-2.97540.39831220.34425852707100
2.9754-3.04460.37841290.321226282757100
3.0446-3.12070.34531250.298126202745100
3.1207-3.2050.35551300.281726022732100
3.205-3.29930.32271440.251326272771100
3.2993-3.40570.28311240.232126102734100
3.4057-3.52740.29391430.229126202763100
3.5274-3.66850.29611320.214826132745100
3.6685-3.83530.28021780.215225852763100
3.8353-4.03730.24161590.211226242783100
4.0373-4.28990.25361290.205626282757100
4.2899-4.62060.23811320.197926702802100
4.6206-5.08460.27751390.199926482787100
5.0846-5.8180.31271340.230427092843100
5.818-7.32140.25141420.233226932835100
7.3214-37.81490.17951740.17332746292098

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