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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


negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin assembly / subtelomeric heterochromatin assembly / nucleosomal DNA binding / spermatid development / nucleus organization / oogenesis ...negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin assembly / subtelomeric heterochromatin assembly / nucleosomal DNA binding / spermatid development / nucleus organization / oogenesis / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / single fertilization / 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 / DNA replication-independent chromatin assembly / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / embryo implantation / Meiotic synapsis / heterochromatin assembly => GO:0031507 / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / DNA replication-dependent chromatin assembly / DNA methylation / HCMV Late Events / innate immune response in mucosa / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Condensation of Prophase Chromosomes / PRC2 methylates histones and DNA / Defective pyroptosis / euchromatin / RNA Polymerase I Promoter Escape / HDACs deacetylate histones / nuclear chromosome / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / Nonhomologous End-Joining (NHEJ) / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / DNA-templated transcription, initiation / Metalloprotease DUBs / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / DNA Damage/Telomere Stress Induced Senescence / osteoblast differentiation / lipopolysaccharide binding / G2/M DNA damage checkpoint / nucleosome assembly / RMTs methylate histone arginines / HCMV Early Events / multicellular organism growth / HDMs demethylate histones / Pre-NOTCH Transcription and Translation / Meiotic recombination / PKMTs methylate histone lysines / nucleosome / Activation of anterior HOX genes in hindbrain development during early embryogenesis / UCH proteinases / Transcriptional regulation of granulopoiesis / male gonad development / E3 ubiquitin ligases ubiquitinate target proteins / cell population proliferation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / chromosome, telomeric region / killing of cells of another organism / positive regulation of cell growth / Oxidative Stress Induced Senescence / antibacterial humoral response / Estrogen-dependent gene expression / antimicrobial humoral immune response mediated by antimicrobial peptide / Ub-specific processing proteases / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / protein domain specific binding / protein-containing complex / RNA binding / DNA binding / extracellular space / extracellular exosome / membrane / extracellular region / nucleoplasm / nucleus / cytosol
Similarity search - Function
Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / C-terminus of histone H2A / Histone H2A, C-terminal domain / Histone 2A ...Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / C-terminus of histone H2A / Histone H2A, C-terminal domain / Histone 2A / Histone H2A / Histone H4 signature. / Histone H4, conserved site / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF) / 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 (> 100) / DNA (> 10) / DNA / 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

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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
Water0
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
γ
α
β
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:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA37 - 133
211chain EE38 - 133
112chain BB20 - 102
212chain FF24 - 102
113chain CC14 - 118
213chain GG15 - 118
114chain DD33 - 124
214chain HH33 - 124
115chain II1 - 146
215chain JJ147 - 292

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: 0

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
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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