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- PDB-4h9q: Complex structure 4 of DAXX(E225A)/H3.3(sub5)/H4 -

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Basic information

Entry
Database: PDB / ID: 4h9q
TitleComplex structure 4 of DAXX(E225A)/H3.3(sub5)/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 / 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 / transcription regulator inhibitor activity / 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 / 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 / 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 / embryo implantation / Meiotic synapsis / Inhibition of DNA recombination at telomere / 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 chromatin organization proteins / SUMOylation of transcription cofactors / 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 / multicellular organism growth / PML body / 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 / HCMV Early Events / Transcriptional regulation of granulopoiesis / nucleosome assembly / male gonad development / transcription corepressor activity / osteoblast differentiation / structural constituent of chromatin / p53 binding / Regulation of TP53 Degradation / nucleosome / 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 / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / cellular response to heat / Processing of DNA double-strand break ends / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / 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 / 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: 1.95 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)52,04312
Polymers51,1883
Non-polymers8559
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14960 Å2
ΔGint-129 kcal/mol
Surface area18930 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)104,08624
Polymers102,3776
Non-polymers1,70918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area31400 Å2
ΔGint-262 kcal/mol
Surface area36380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.522, 107.522, 90.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Histone H3.3


Mass: 15257.816 Da / Num. of mol.: 1 / Mutation: 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: E48C
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.: 9 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.55 Å3/Da / Density % sol: 51.84 %
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: NSLS / Beamline: X29A / Wavelength: 0.979 Å
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 39075 / Num. obs: 39075 / % possible obs: 99.7 % / 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: 1.95→38.873 Å / SU ML: 0.43 / σ(F): 1.34 / σ(I): 8.7 / Phase error: 23.07 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 1947 4.99 %RANDOM
Rwork0.1909 ---
all0.2209 39075 --
obs0.1924 38989 99.65 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.687 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.5676 Å20 Å20 Å2
2---6.5676 Å20 Å2
3---13.1351 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3095 0 45 215 3355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073174
X-RAY DIFFRACTIONf_angle_d0.9654277
X-RAY DIFFRACTIONf_dihedral_angle_d14.8631227
X-RAY DIFFRACTIONf_chiral_restr0.067476
X-RAY DIFFRACTIONf_plane_restr0.004552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00010.34351320.25662590X-RAY DIFFRACTION100
2.0001-2.05420.25061300.21712623X-RAY DIFFRACTION100
2.0542-2.11460.27151620.19352565X-RAY DIFFRACTION100
2.1146-2.18290.2021220.19942649X-RAY DIFFRACTION100
2.1829-2.26090.2851360.19852601X-RAY DIFFRACTION100
2.2609-2.35140.20611320.20442627X-RAY DIFFRACTION100
2.3514-2.45840.21071350.19162642X-RAY DIFFRACTION100
2.4584-2.5880.23291450.19942629X-RAY DIFFRACTION100
2.588-2.75010.20931400.20552635X-RAY DIFFRACTION100
2.7501-2.96230.25921470.20712639X-RAY DIFFRACTION100
2.9623-3.26030.27181330.2042673X-RAY DIFFRACTION100
3.2603-3.73170.19371540.18052669X-RAY DIFFRACTION100
3.7317-4.70030.19041280.15572730X-RAY DIFFRACTION100
4.7003-38.8730.20721510.19852770X-RAY DIFFRACTION97
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)
14.90932.5754-3.16694.5954-2.50167.4431-0.09410.35510.5646-0.17640.0085-0.1379-0.44140.06220.14030.2040.0177-0.04820.31130.03350.378423.6442-28.36493.6185
24.34391.3367-1.08128.6273-1.81734.87870.1728-0.4518-0.46950.4771-0.1783-0.26470.3465-0.26620.02410.2498-0.0242-0.05360.39030.09910.273522.2725-50.252519.3123
37.89365.5331-4.97524.4637-4.4214.3211-0.053-1.0605-1.4852-0.805-0.7282-1.09961.73970.40560.67050.45070.04750.03040.54090.13460.713924.6898-57.262410.7334
46.9499-5.1086-2.29725.60262.31142.2159-0.0428-0.02260.20860.0063-0.1081-0.1626-0.2122-0.09730.09110.23460.0196-0.05120.32080.00070.230211.332-38.258414.88
52.878-1.69781.29693.8256-0.47540.4995-0.3877-0.8480.11720.82690.27440.70670.20640.23430.12080.43970.19340.04380.6301-0.14030.3863-1.1371-28.118928.3117
69.4322-2.20850.90525.6948-0.48637.3245-0.1841-0.2743-0.47970.10830.15970.6979-0.111-0.50780.07790.24320.0836-0.01410.445-0.02590.3979-2.8449-39.797221.008
74.21342.3656-4.19773.7158-2.6634.0418-0.3260.112-0.9130.0292-0.54780.03660.19610.37480.82350.4277-0.0098-0.15790.59150.01470.615817.2721-42.006435.4184
85.3150.17261.58785.4322-2.06662.2278-0.03-1.01580.78970.9866-0.022-0.3648-0.55760.22580.08140.370.0665-0.09160.5309-0.1380.319411.6523-31.107325.6647
93.3809-1.5261-0.51484.59973.3876.8239-0.1554-0.4991-0.27490.37370.0941-0.01270.27140.05890.00460.15820.0022-0.01420.27810.08080.211312.1017-49.691216.9953
107.2589-2.0294-0.00496.86351.10733.1120.12270.164-0.1674-0.2395-0.1887-0.3370.05740.16750.06910.18330.01140.01450.23270.01680.148213.0456-48.62553.523
112.77633.4282-1.16257.037-2.71512.9261-0.2130.086-0.2236-0.3124-0.0135-0.54860.02980.35810.26890.1439-0.00020.00890.42180.01550.348234.8632-36.82444.3926
124.26540.63490.20763.4218-4.15484.3668-0.3432-0.08490.3070.82690.2303-0.6353-0.5698-0.02810.19620.2447-0.0256-0.04620.34680.02240.422831.9498-29.68758.3325
133.7644-1.1105-0.99150.04240.34961.35810.0550.11851.412-0.1025-0.0688-0.488-0.4192-0.15930.00050.34170.0414-0.05330.35350.05660.670110.1362-17.61645.3408
146.0258-2.4296-1.43921.58670.98541.6016-0.0046-0.381.6138-0.1752-0.0826-0.9234-0.2580.20280.13620.2920.0585-0.05160.3772-0.11560.80175.5426-16.470313.8039
151.1281-1.9386-1.03556.6267-0.09721.9528-0.1531-1.04591.08390.4599-0.5667-1.1505-0.55190.49570.21350.31640.0486-0.24370.3945-0.44080.8719-2.1973-10.098521.5604
169.0031-7.2917-5.03437.76975.07413.2907-0.0241-0.12360.4545-0.0138-0.14440.2236-0.114-0.21920.24640.25730.0264-0.08680.3706-0.08560.4208-1.1447-23.568413.2272
173.01711.58560.82573.33640.86361.8049-0.09570.1805-0.0088-0.4647-0.1143-0.13340.09850.25360.19220.32330.03910.00830.32890.04030.270214.5121-46.1233-3.0554
181.7168-2.6546-2.28456.28724.06632.5734-0.2337-0.4733-0.39040.606-0.36450.67890.6194-0.59410.58950.202-0.02980.01380.39730.04090.24652.749-52.99318.4727
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 37:63)
2X-RAY DIFFRACTION2chain 'A' and (resseq 64:78)
3X-RAY DIFFRACTION3chain 'A' and (resseq 79:85)
4X-RAY DIFFRACTION4chain 'A' and (resseq 86:109)
5X-RAY DIFFRACTION5chain 'A' and (resseq 110:120)
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 48:75)
10X-RAY DIFFRACTION10chain 'B' and (resseq 76:102)
11X-RAY DIFFRACTION11chain 'C' and (resseq 182:220)
12X-RAY DIFFRACTION12chain 'C' and (resseq 221:242)
13X-RAY DIFFRACTION13chain 'C' and (resseq 243:264)
14X-RAY DIFFRACTION14chain 'C' and (resseq 265:285)
15X-RAY DIFFRACTION15chain 'C' and (resseq 286:305)
16X-RAY DIFFRACTION16chain 'C' and (resseq 306:333)
17X-RAY DIFFRACTION17chain 'C' and (resseq 334:354)
18X-RAY DIFFRACTION18chain 'C' and (resseq 355:386)

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