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- PDB-4h9s: Complex structure 6 of DAXX/H3.3(sub7)/H4 -

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Basic information

Entry
Database: PDB / ID: 4h9s
TitleComplex structure 6 of DAXX/H3.3(sub7)/H4
Components
  • Death domain-associated protein 6
  • Histone H3.3
  • Histone H4
KeywordsDNA BINDING PROTEIN/APOPTOSIS / histone chaperone / DNA BINDING PROTEIN-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 / : / 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 / : / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / oocyte maturation / nucleosomal DNA binding / nuclear androgen receptor binding / androgen receptor signaling pathway / nucleus organization / cellular response to cadmium ion / extrinsic apoptotic signaling pathway via death domain receptors / chromosome, centromeric region / protein kinase activator activity / regulation of protein ubiquitination / spermatid development / cellular response to unfolded protein / single fertilization / subtelomeric heterochromatin formation / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / transcription regulator inhibitor activity / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / JNK cascade / heat shock protein binding / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / embryo implantation / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / SUMOylation of transcription cofactors / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / cellular response to copper ion / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / 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 / 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 / Transcriptional regulation by small RNAs / molecular condensate scaffold activity / 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 / PML body / G2/M DNA damage checkpoint / 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 / multicellular organism growth / male gonad development / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / osteoblast differentiation / p53 binding / structural constituent of chromatin / Regulation of TP53 Degradation / transcription corepressor activity / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / 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 / Senescence-Associated Secretory Phenotype (SASP)
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 domain / Histone-fold / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Histone H4 / Histone H3.3 / Death domain-associated protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsElsasser, S.J. / Huang, H. / Lewis, P.W. / Chin, J.W. / Allis, D.C. / Patel, D.J.
CitationJournal: To be Published
Title: DAXX chaperone envelops an H3.3/H4 dimer dictating H3.3-specific read out
Authors: Elsasser, S.J. / Huang, H. / Lewis, P.W. / Chin, J.W. / Allis, D.C. / Patel, D.J.
History
DepositionSep 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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: Histone H3.3
B: Histone H3.3
C: Histone H4
D: Histone H4
E: Death domain-associated protein 6
F: Death domain-associated protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,60311
Polymers100,1286
Non-polymers4755
Water3,099172
1
A: Histone H3.3
C: Histone H4
F: Death domain-associated protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3496
Polymers50,0643
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12710 Å2
ΔGint-101 kcal/mol
Surface area18100 Å2
MethodPISA
2
B: Histone H3.3
D: Histone H4
E: Death domain-associated protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2545
Polymers50,0643
Non-polymers1902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12320 Å2
ΔGint-96 kcal/mol
Surface area18420 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29550 Å2
ΔGint-208 kcal/mol
Surface area32000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.397, 99.165, 100.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone H3.3


Mass: 15328.918 Da / Num. of mol.: 2 / Mutation: A75C, F84W, S96A, Y99F, G102A, A111T, M120F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B / Production host: Escherichia coli (E. coli) / References: UniProt: P84243
#2: Protein Histone H4


Mass: 9409.056 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
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein Death domain-associated protein 6 / Daxx / hDaxx / ETS1-associated protein 1 / EAP1 / Fas death domain-associated protein


Mass: 25326.129 Da / Num. of mol.: 2 / Fragment: UNP residues 178-389
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAXX, BING2, DAP6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UER7
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 30321 / Num. obs: 30321 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 36.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→44.092 Å / SU ML: 0.75 / σ(F): 1.33 / σ(I): 4.8 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 1535 5.07 %RANDOM
Rwork0.1952 ---
obs0.198 30302 99.95 %-
all-30321 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.355 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5691 Å2-0 Å20 Å2
2---3.353 Å20 Å2
3---3.9222 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5879 0 25 172 6076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055974
X-RAY DIFFRACTIONf_angle_d0.9398040
X-RAY DIFFRACTIONf_dihedral_angle_d16.7852331
X-RAY DIFFRACTIONf_chiral_restr0.071913
X-RAY DIFFRACTIONf_plane_restr0.0041042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.68390.28581400.24822581X-RAY DIFFRACTION100
2.6839-2.77980.31131470.24262554X-RAY DIFFRACTION100
2.7798-2.89110.36161370.23652574X-RAY DIFFRACTION100
2.8911-3.02270.2961290.22542601X-RAY DIFFRACTION100
3.0227-3.1820.31321300.23192590X-RAY DIFFRACTION100
3.182-3.38130.26211520.20692579X-RAY DIFFRACTION100
3.3813-3.64220.2461260.18852618X-RAY DIFFRACTION100
3.6422-4.00850.21241300.16842615X-RAY DIFFRACTION100
4.0085-4.58810.20771430.15242639X-RAY DIFFRACTION100
4.5881-5.77840.23581480.1862649X-RAY DIFFRACTION100
5.7784-44.0920.23851530.20292767X-RAY DIFFRACTION100

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