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- PDB-4h9r: Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4 -

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Basic information

Entry
Database: PDB / ID: 4h9r
TitleComplex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4
Components
  • Death domain-associated protein 6
  • Histone H3.3H3F3A
  • 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 / transcription regulator inhibitor activity / nuclear androgen receptor binding / protein kinase activator activity / androgen receptor signaling pathway ...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 / transcription regulator inhibitor activity / nuclear androgen receptor binding / protein kinase activator activity / androgen receptor signaling pathway / chromosome, centromeric region / regulation of protein ubiquitination / extrinsic apoptotic signaling pathway via death domain receptors / nucleosomal DNA binding / positive regulation of protein kinase activity / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / cellular response to unfolded protein / 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 cadmium ion / cellular response to copper ion / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / heat shock protein binding / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / molecular condensate scaffold activity / 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 / 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 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / PML body / PKMTs methylate histone lysines / 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 / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / Regulation of TP53 Degradation / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / regulation of gene expression / Oxidative Stress Induced Senescence / regulation of apoptotic process / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / transcription coactivator activity / nuclear body / chromatin remodeling / positive regulation of protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / regulation of DNA-templated transcription
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: 2.197 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 H4
C: Death domain-associated protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7729
Polymers51,2023
Non-polymers5706
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14540 Å2
ΔGint-120 kcal/mol
Surface area18790 Å2
MethodPISA
2
A: Histone H3.3
B: Histone H4
C: Death domain-associated protein 6
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)103,54418
Polymers102,4056
Non-polymers1,14012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area30350 Å2
ΔGint-245 kcal/mol
Surface area36310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.701, 107.701, 90.711
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-572-

HOH

21C-573-

HOH

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Components

#1: Protein Histone H3.3 / H3F3A


Mass: 15271.842 Da / Num. of mol.: 1 / Mutation: G90A, 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: 24667.293 Da / Num. of mol.: 1 / Fragment: UNP residues 178-389 / Mutation: E48A
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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 1.6 M Na/K-phosphate, pH 6.8, 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: 2.197→50 Å / Num. all: 27814 / Num. obs: 27814 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 33.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.197→38.968 Å / SU ML: 0.21 / σ(F): 1.36 / σ(I): 3.7 / Phase error: 23.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2302 1394 5.03 %RANDOM
Rwork0.1838 ---
obs0.1863 27739 99.91 %-
all-27814 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.197→38.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3092 0 30 228 3350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093159
X-RAY DIFFRACTIONf_angle_d1.114255
X-RAY DIFFRACTIONf_dihedral_angle_d14.6361225
X-RAY DIFFRACTIONf_chiral_restr0.084477
X-RAY DIFFRACTIONf_plane_restr0.005550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.197-2.27560.26081150.23312578X-RAY DIFFRACTION99
2.2756-2.36670.28421340.20982580X-RAY DIFFRACTION100
2.3667-2.47440.25581250.20392615X-RAY DIFFRACTION100
2.4744-2.60490.23691720.19942570X-RAY DIFFRACTION100
2.6049-2.7680.24911430.20032610X-RAY DIFFRACTION100
2.768-2.98170.28171270.20292614X-RAY DIFFRACTION100
2.9817-3.28160.26061540.19372615X-RAY DIFFRACTION100
3.2816-3.75610.21641350.16572647X-RAY DIFFRACTION100
3.7561-4.7310.18291380.14882691X-RAY DIFFRACTION100
4.731-38.9680.22821510.19162825X-RAY DIFFRACTION100
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)
16.06464.19083.65543.02963.52499.09710.47750.0211-0.8852-0.42880.0898-2.7402-0.23120.7569-0.62970.62960.04530.0540.5483-0.01590.9808-21.0696-26.0509-26.2661
27.466-0.3323-4.75594.1945-0.23434.9786-0.37330.1351-0.5029-0.222-0.2464-0.68870.47490.30270.6270.34540.01280.02620.20620.04050.391-32.0828-22.2372-15.986
38.9073-1.28052.47053.6798-2.06671.5328-0.0177-0.9125-0.390.5690.13350.32340.0018-0.245-0.1030.41510.01990.12580.23630.07290.2378-48.7735-23.1284-2.68
45.0438-4.3015-5.86053.95174.14679.2637-0.71570.3113-0.98020.33220.50290.74810.5027-1.33330.19280.506-0.02020.06640.45220.0990.663-58.5572-23.2034-10.0379
58.23196.55513.5585.04913.29414.1207-0.1167-0.114-0.27170.0914-0.1541-0.5281-0.27820.22790.16470.3758-0.02770.00340.17990.07090.2467-38.1341-11.4004-7.525
60.5818-0.5079-0.15570.45050.12890.04920.1436-0.6701-0.04371.0299-0.2358-0.51170.18320.12040.05511.1219-0.5383-0.56680.4331-0.00690.2211-26.12880.86416.0114
72.95134.05240.00565.62040.22279.17050.5648-0.51530.68650.4838-0.37940.7970.0270.0556-0.14370.5219-0.11210.00010.33370.01340.3376-39.31252.6372-1.0224
83.15350.1499-3.2141-0.0302-0.14343.2074-0.3209-0.3785-0.0584-0.08530.21610.24410.74580.25670.23870.6121-0.0683-0.11840.38250.16260.4709-36.6301-15.92137.2067
94.48151.24191.82274.5002-0.91854.68440.0227-0.1805-0.08880.4648-0.11890.2444-0.1406-0.14920.05540.2536-0.00730.07470.1059-0.0110.202-47.2959-12.0753-9.8526
107.1217-3.6651-2.08822.28090.99122.4520.06850.497-0.6652-0.0036-0.33840.33460.4129-0.07270.24610.55180.02590.06910.1453-0.02040.4256-36.8701-35.0091-18.4269
114.8797-1.2355-6.25614.06950.83457.90380.0846-0.9636-0.74920.0247-0.2288-0.49320.25250.84750.18590.39210.07020.0610.23180.06650.444-30.2561-31.946-14.142
120.76951.24530.57774.63971.48821.9995-0.09590.3216-0.7638-0.05160.164-1.60580.18060.4737-0.09530.4577-0.05050.02270.38560.00310.966-16.9216-8.0294-13.6153
133.18491.888-2.90972.957-0.41053.5849-0.1414-1.0763-0.86420.9403-0.5669-1.97150.1310.71180.48110.6247-0.1222-0.52310.38450.27381.3703-13.41040.4028-0.3975
147.24854.84564.17495.39692.75593.0727-0.20040.14280.30060.218-0.0025-0.7246-0.33460.34270.24610.4379-0.0559-0.12170.25690.10690.6082-20.14222.3273-8.0632
155.3766-2.65241.93825.4665-1.19823.6542-0.11260.7584-0.2057-0.3733-0.1309-0.19340.4075-0.05980.21280.3083-0.05550.05360.2649-0.02940.2166-45.5449-14.717-25.3953
164.76122.67845.16342.92322.31835.086-0.3168-0.62790.87780.8509-0.36670.6718-0.7044-0.53690.62950.6151-0.02470.12040.3993-0.03570.3583-52.9922-2.8894-4.069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 77 )
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 85 )
5X-RAY DIFFRACTION5chain 'A' and (resid 86 through 110 )
6X-RAY DIFFRACTION6chain 'A' and (resid 111 through 120 )
7X-RAY DIFFRACTION7chain 'A' and (resid 121 through 134 )
8X-RAY DIFFRACTION8chain 'B' and (resid 20 through 41 )
9X-RAY DIFFRACTION9chain 'B' and (resid 42 through 102 )
10X-RAY DIFFRACTION10chain 'C' and (resid 182 through 220 )
11X-RAY DIFFRACTION11chain 'C' and (resid 221 through 242 )
12X-RAY DIFFRACTION12chain 'C' and (resid 243 through 285 )
13X-RAY DIFFRACTION13chain 'C' and (resid 286 through 299 )
14X-RAY DIFFRACTION14chain 'C' and (resid 300 through 333 )
15X-RAY DIFFRACTION15chain 'C' and (resid 334 through 354 )
16X-RAY DIFFRACTION16chain 'C' and (resid 355 through 386 )

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