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- PDB-4h9o: Complex structure 2 of DAXX/H3.3(sub5,G90M)/H4 -

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Basic information

Entry
Database: PDB / ID: 4h9o
TitleComplex structure 2 of DAXX/H3.3(sub5,G90M)/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 / 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 / cellular response to unfolded protein / RNA polymerase II core promoter sequence-specific 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 / nucleosomal DNA binding / 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 / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SUMOylation of transcription cofactors / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / molecular condensate scaffold activity / PRC2 methylates histones and DNA / Defective pyroptosis / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / 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 / Meiotic recombination / RMTs methylate histone arginines / 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
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: 2.053 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 10, 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 H4
C: Death domain-associated protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,27013
Polymers51,3213
Non-polymers95010
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15170 Å2
ΔGint-134 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.691, 107.691, 90.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-571-

HOH

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Components

#1: Protein Histone H3.3


Mass: 15331.961 Da / Num. of mol.: 1 / Mutation: G90M, 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: 11263.231 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
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: 24725.328 Da / Num. of mol.: 1 / 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.: 10 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 33889 / Num. obs: 33889 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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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: 2.053→38.075 Å / SU ML: 0.56 / σ(F): 1.36 / σ(I): 4.2 / Phase error: 21.01 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 1710 5.06 %RANDOM
Rwork0.1822 ---
all0.2245 33826 --
obs0.1843 33826 99.74 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.02 Å2 / ksol: 0.365 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.596 Å2-0 Å20 Å2
2---4.596 Å20 Å2
3---9.1921 Å2
Refinement stepCycle: LAST / Resolution: 2.053→38.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3086 0 50 224 3360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083169
X-RAY DIFFRACTIONf_angle_d1.0054271
X-RAY DIFFRACTIONf_dihedral_angle_d15.3221223
X-RAY DIFFRACTIONf_chiral_restr0.067476
X-RAY DIFFRACTIONf_plane_restr0.004549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.053-2.11350.28191540.22852563X-RAY DIFFRACTION98
2.1135-2.18170.26561430.21172617X-RAY DIFFRACTION100
2.1817-2.25970.24451340.20172645X-RAY DIFFRACTION100
2.2597-2.35010.2551530.20922640X-RAY DIFFRACTION100
2.3501-2.45710.26381300.19512666X-RAY DIFFRACTION100
2.4571-2.58660.25581520.20132619X-RAY DIFFRACTION100
2.5866-2.74860.23151530.19882665X-RAY DIFFRACTION100
2.7486-2.96080.2371290.18782683X-RAY DIFFRACTION100
2.9608-3.25860.24641270.18962706X-RAY DIFFRACTION100
3.2586-3.72970.19571410.1742699X-RAY DIFFRACTION100
3.7297-4.69770.17851540.14622743X-RAY DIFFRACTION100
4.6977-38.0750.23471400.18442870X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9060.4121-3.79599.6764-2.75287.96530.5310.43142.031-0.3861-0.3884-0.5905-0.656-0.2134-0.0850.4869-0.1466-0.03440.64850.10770.946326.3027-22.1173-3.71
25.69492.6523-4.24618.0506-5.66665.08740.01810.12240.49380.2484-0.2304-0.5153-0.63260.43780.20570.17050.0378-0.00660.3176-0.01960.42522.2883-32.52487.8501
35.51530.80840.28736.2421-0.27255.18270.1983-0.5152-0.50570.8177-0.3152-0.33830.1198-0.03380.19940.224-0.0324-0.05320.33110.10030.260522.2419-50.202319.8729
45.24125.1292-1.58625.1214-2.1413.28930.5322-0.832-1.2592-0.1445-1.0485-1.62981.48570.38880.63990.41830.071-0.03120.5370.18640.687624.572-57.230911.2296
52.4652-1.1196-0.43492.2780.30042.0282-0.3504-0.90250.32030.20510.2199-0.046-0.2546-0.00390.10790.27280.0812-0.09980.4663-0.0820.26437.3797-34.845319.6397
67.6635-2.13760.11772.7322-0.17138.8907-0.503-0.6985-0.56290.26470.64030.6890.0794-0.5671-0.16180.25770.109-0.02520.5707-0.0150.3399-2.8273-39.593921.4654
79.2048-1.0701-6.43375.9851.10484.5069-0.40550.5276-0.50850.26210.0641-0.19110.98260.5990.23940.42270.0613-0.20730.6415-0.14930.615917.2317-41.9835.9323
80.6607-0.7037-0.19723.931-1.74132.4879-0.3272-1.12510.78610.61690.0418-0.3344-0.4507-0.03820.28350.37340.1598-0.16810.7593-0.25020.397411.7648-31.040125.8939
94.1113-1.4056-0.81183.64453.71199.2009-0.1781-0.5454-0.45470.2822-0.0814-0.13920.3115-0.16950.1550.14490.004-0.02630.27740.1210.192513.8768-51.203414.7659
106.8172-3.8303-2.89248.47383.10864.5379-0.00660.006-0.2301-0.3937-0.16960.0987-0.138-0.07380.22460.2145-0.0116-0.02380.25840.01420.166510.0177-45.6454.2183
115.78984.9414-2.18854.5483-3.0243.7927-0.53290.3642-0.1221-0.5680.4861-0.3901-0.01370.24550.07540.22-0.10650.00730.50390.02980.323236.8925-29.742-0.5837
124.56634.3005-2.18944.9296-1.89744.7564-0.0253-0.1549-0.25950.0791-0.5426-1.290.35360.73580.56650.24090.0786-0.01270.46580.15340.535631.2089-49.858613.9264
137.1331.8571-0.67853.9778-5.04286.5243-0.1138-0.2250.25440.63610.0808-0.2771-0.5006-0.02340.07670.2112-0.0362-0.00530.3330.02410.338631.9088-29.98878.4829
147.21824.413-2.25446.3604-2.66135.70440.16830.71161.90280.24270.0468-0.2847-0.867-0.0339-0.23840.393-0.02140.00480.44560.04880.901821.1096-20.6262.6288
154.5428-6.5747-3.90739.96043.89579.52880.34710.3352.4453-0.3149-0.1536-1.767-0.58490.0502-0.21790.39560.1103-0.06270.5354-0.02510.7571-1.3322-14.8198.0499
165.1465-3.7247-0.9414.0798-0.36522.84680.0456-0.32172.1995-0.18790.038-1.4428-0.24490.2872-0.04360.31350.031-0.01170.4028-0.08681.01545.4606-16.504113.9083
173.7737-3.919-0.39464.269-0.11731.4881-0.0535-0.47651.85380.25570.0474-0.9591-0.77410.23150.076-0.03620.0834-0.24310.5783-0.45411.2062-2.3349-9.97721.5512
187.1763-6.6528-7.1715.81456.80167.30170.02760.20320.55-0.0205-0.2439-0.0512-0.1401-0.41070.21870.2360.0313-0.0820.3556-0.05420.4919-0.0916-24.31112.4922
194.46843.49861.03125.8536-0.29292.9262-0.20950.2488-0.1938-0.8292-0.0832-0.32130.00650.3640.2660.2450.0860.02540.29210.01050.221614.4869-48.0797-3.0266
202.922-2.5629-2.93524.894.99569.2463-0.255-0.893-0.58930.5322-0.08080.4340.3132-0.48590.33340.26420.02960.01590.53730.0830.19262.7521-52.851919.068
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 38:47)
2X-RAY DIFFRACTION2chain 'A' and (resseq 48:63)
3X-RAY DIFFRACTION3chain 'A' and (resseq 64:78)
4X-RAY DIFFRACTION4chain 'A' and (resseq 79:85)
5X-RAY DIFFRACTION5chain 'A' and (resseq 86:120)
6X-RAY DIFFRACTION6chain 'A' and (resseq 121:134)
7X-RAY DIFFRACTION7chain 'B' and (resseq 20:30)
8X-RAY DIFFRACTION8chain 'B' and (resseq 31:47)
9X-RAY DIFFRACTION9chain 'B' and (resseq 48:82)
10X-RAY DIFFRACTION10chain 'B' and (resseq 83:102)
11X-RAY DIFFRACTION11chain 'C' and (resseq 182:206)
12X-RAY DIFFRACTION12chain 'C' and (resseq 207:220)
13X-RAY DIFFRACTION13chain 'C' and (resseq 221:242)
14X-RAY DIFFRACTION14chain 'C' and (resseq 243:254)
15X-RAY DIFFRACTION15chain 'C' and (resseq 255:264)
16X-RAY DIFFRACTION16chain 'C' and (resseq 265:285)
17X-RAY DIFFRACTION17chain 'C' and (resseq 286:305)
18X-RAY DIFFRACTION18chain 'C' and (resseq 306:335)
19X-RAY DIFFRACTION19chain 'C' and (resseq 336:354)
20X-RAY DIFFRACTION20chain 'C' and (resseq 355:386)

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