[English] 日本語
Yorodumi
- PDB-4hga: Structure of the variant histone H3.3-H4 heterodimer in complex w... -

+
Open data


ID or keywords:

Loading...

-
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 H3.3
  • 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 / 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 / pericentric heterochromatin formation / inner kinetochore ...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 / 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 / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / oocyte maturation / nucleosomal DNA binding / nuclear androgen receptor binding / cellular response to cadmium ion / nucleus organization / spermatid development / androgen receptor signaling pathway / protein kinase activator activity / chromosome, centromeric region / extrinsic apoptotic signaling pathway via death domain receptors / single fertilization / regulation of protein ubiquitination / cellular response to unfolded protein / negative regulation of megakaryocyte differentiation / subtelomeric heterochromatin formation / protein localization to CENP-A containing chromatin / transcription regulator inhibitor activity / RNA polymerase II core promoter sequence-specific DNA binding / 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 / cellular response to copper ion / heat shock protein binding / 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 / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of transcription cofactors / 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 / 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 / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / molecular condensate scaffold activity / 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 / PML body / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / male gonad development / transcription corepressor activity / osteoblast differentiation / structural constituent of chromatin / p53 binding / Regulation of TP53 Degradation / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / positive regulation of protein phosphorylation / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / cellular response to heat / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / regulation of gene expression / positive regulation of cell growth
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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more