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- PDB-4hga: Structure of the variant histone H3.3-H4 heterodimer in complex w... -

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Basic information

Entry
Database: PDB / ID: 4hga
TitleStructure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX
Components
  • Death domain-associated protein 6
  • Histone H3.3H3F3A
  • Histone H4
KeywordsCHAPERONE/APOPTOSIS / histone chaperone / CHAPERONE-APOPTOSIS complex
Function / homology
Function and homology information


cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / SUMO-modified protein reader activity / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / cellular response to sodium arsenite / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation ...cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / SUMO-modified protein reader activity / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / cellular response to sodium arsenite / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / transcription regulator inhibitor activity / oocyte maturation / nuclear androgen receptor binding / nucleus organization / protein kinase activator activity / androgen receptor signaling pathway / chromosome, centromeric region / regulation of protein ubiquitination / spermatid development / extrinsic apoptotic signaling pathway via death domain receptors / single fertilization / subtelomeric heterochromatin formation / negative regulation of megakaryocyte differentiation / positive regulation of protein kinase activity / RNA polymerase II core promoter sequence-specific DNA binding / cellular response to unfolded protein / nucleosomal DNA binding / 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 / JNK cascade / Deposition of new CENPA-containing nucleosomes at the centromere / cellular response to copper ion / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / heat shock protein binding / Meiotic synapsis / cellular response to cadmium ion / telomere organization / embryo implantation / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / SUMOylation of transcription cofactors / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / molecular condensate scaffold activity / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / 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 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / PML body / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / osteoblast differentiation / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / transcription corepressor activity / male gonad development / nucleosome / nucleosome assembly / Regulation of TP53 Degradation / p53 binding / 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 / cellular response to heat / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Processing of DNA double-strand break ends / histone binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / regulation of gene expression / regulation of apoptotic process
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2170 / Daxx, N-terminal Rassf1C-interacting domain / Daxx, N-terminal domain superfamily / Daxx, histone-binding domain / Daxx, histone-binding domain superfamily / Daxx N-terminal Rassf1C-interacting domain / Death domain-associated protein 6, histone binding domain / Histone, subunit A / Histone, subunit A / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2170 / Daxx, N-terminal Rassf1C-interacting domain / Daxx, N-terminal domain superfamily / Daxx, histone-binding domain / Daxx, histone-binding domain superfamily / Daxx N-terminal Rassf1C-interacting domain / Death domain-associated protein 6, histone binding domain / Histone, subunit A / Histone, subunit A / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Histone H4, conserved site / Histone H4 signature. / 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-like fold domain / 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 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TETRACHLOROPLATINATE(II) / Histone H4 / Histone H3.3 / Death domain-associated protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.799 Å
AuthorsLiu, C.P. / Xiong, C.Y. / Wang, M.Z. / Yu, Z.L. / Yang, N. / Chen, P. / Zhang, Z.G. / Li, G.H. / Xu, R.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX.
Authors: Liu, C.P. / Xiong, C.Y. / Wang, M.Z. / Yu, Z.L. / Yang, N. / Chen, P. / Zhang, Z.G. / Li, G.H. / Xu, R.M.
History
DepositionOct 7, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Death domain-associated protein 6
B: Histone H3.3
C: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9087
Polymers51,5613
Non-polymers1,3484
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-138 kcal/mol
Surface area18090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.103, 72.103, 323.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Death domain-associated protein 6 / Daxx / hDaxx / ETS1-associated protein 1 / EAP1 / Fas death domain-associated protein


Mass: 24805.361 Da / Num. of mol.: 1 / Fragment: HISTONE BINDING DOMAIN, UNP RESIDUES 184-390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAXX, BING2, DAP6 / Plasmid: PGEX-6P-Xu / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3) RIL / References: UniProt: Q9UER7
#2: Protein Histone H3.3 / H3F3A


Mass: 15360.983 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3) RIL / References: UniProt: P84243
#3: Protein Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 1
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: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3) RIL / References: UniProt: P62805
#4: Chemical
ChemComp-PC4 / TETRACHLOROPLATINATE(II)


Mass: 336.890 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl4Pt
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.1M HEPES-Na, pH 7.6, 23% (v/v) PEG 3350, 0.25M Ammonium acetate, 1% Tacsimate pH 7.0, 6% ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.799→50 Å / Num. all: 13301 / Num. obs: 13274 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 21.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 1.91 / Num. unique all: 1254 / % possible all: 99.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.799→44.934 Å / SU ML: 0.34 / σ(F): 1.36 / Phase error: 24.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 635 4.82 %RANDOM
Rwork0.2076 ---
all0.2105 13301 --
obs0.2105 13183 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.799→44.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 13 28 3081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063090
X-RAY DIFFRACTIONf_angle_d0.9054149
X-RAY DIFFRACTIONf_dihedral_angle_d16.0011228
X-RAY DIFFRACTIONf_chiral_restr0.059462
X-RAY DIFFRACTIONf_plane_restr0.003541
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7993-3.01540.32891460.2852238699
3.0154-3.31870.29081140.23172442100
3.3187-3.79880.28241180.20392484100
3.7988-4.78520.23151190.1822527100
4.7852-44.93970.2651380.19782709100
Refinement TLS params.Method: refined / Origin x: 39.1942 Å / Origin y: 22.8178 Å / Origin z: 150.9987 Å
111213212223313233
T0.5014 Å20.0862 Å2-0.0181 Å2-0.3532 Å2-0.1051 Å2--0.3991 Å2
L2.3709 °2-0.0084 °20.0192 °2-2.6803 °2-0.6984 °2--5.0874 °2
S-0.2657 Å °-0.1825 Å °0.0569 Å °0.4847 Å °0.1028 Å °-0.1486 Å °-0.5658 Å °-0.3967 Å °0.114 Å °
Refinement TLS groupSelection details: ALL

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