[English] 日本語
Yorodumi
- PDB-4h9p: Complex structure 3 of DAXX/H3.3(sub5,G90A)/H4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4h9p
TitleComplex structure 3 of DAXX/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 / 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 / RNA polymerase II core promoter sequence-specific DNA binding / cellular response to unfolded protein / nucleosomal 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 / 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 / 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 / molecular condensate scaffold activity / 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 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / PML body / 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 / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / 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: 2.198 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)51,92510
Polymers51,2603
Non-polymers6657
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14660 Å2
ΔGint-118 kcal/mol
Surface area19030 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)103,85020
Polymers102,5216
Non-polymers1,33014
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area30920 Å2
ΔGint-244 kcal/mol
Surface area36460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.715, 107.715, 90.776
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
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: 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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 1.8 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
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: 2.198→50 Å / Num. all: 27794 / Num. obs: 27794 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 37.5

-
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: 2.198→38.08 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2423 1393 5.02 %
Rwork0.1866 --
all0.2423 27794 -
obs0.1894 27729 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.198→38.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 35 239 3370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083167
X-RAY DIFFRACTIONf_angle_d1.0824267
X-RAY DIFFRACTIONf_dihedral_angle_d15.1291227
X-RAY DIFFRACTIONf_chiral_restr0.086477
X-RAY DIFFRACTIONf_plane_restr0.005552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.198-2.27680.38331170.33212582X-RAY DIFFRACTION100
2.2768-2.3680.33761200.23352592X-RAY DIFFRACTION100
2.368-2.47580.29471420.20572594X-RAY DIFFRACTION100
2.4758-2.60630.26431590.19712586X-RAY DIFFRACTION100
2.6063-2.76960.26611540.19792594X-RAY DIFFRACTION100
2.7696-2.98340.26791270.2042610X-RAY DIFFRACTION100
2.9834-3.28350.26761490.1892617X-RAY DIFFRACTION100
3.2835-3.75850.23041310.16912654X-RAY DIFFRACTION100
3.7585-4.73450.18821450.14842686X-RAY DIFFRACTION100
4.7345-46.3190.22521490.18442821X-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)
14.80720.4744-1.84094.4504-1.39037.52580.05630.70951.0612-0.2960.1556-0.2142-1.1343-0.0057-0.16680.3438-0.044-0.02110.40960.05830.588423.5645-28.14282.7283
24.96710.26211.5388.70833.18174.31970.1573-0.6242-0.36070.8865-0.3896-0.5770.165-0.02680.22780.1996-0.0299-0.05380.31260.11390.220422.7373-49.352420.3501
35.58180.76840.30125.5434-5.73086.099-0.0204-0.509-0.5455-0.9347-0.1323-0.59861.4362-0.55710.15130.41880.0758-0.02060.53690.09860.582424.4394-58.395712.3775
45.9754-6.2949-2.43657.65022.24343.2246-0.2936-0.0690.26590.1346-0.0065-0.2913-0.0736-0.22490.17720.15830.0156-0.07350.2998-0.02280.197211.3932-38.00815.3589
51.69970.23661.76130.2160.63052.574-0.71-1.450.32370.85720.27110.4369-0.86280.31290.2765-0.40740.5726-1.09860.9462-0.1792-0.5161-0.7832-25.827128.7876
65.3164-2.4383-0.07426.4211-0.69079.6441-0.1895-0.1899-0.70210.59150.68150.64670.17150.0665-0.4710.27640.129-0.05020.4628-0.01220.3259-2.594-39.178721.9178
77.80920.8985-6.18034.2079-0.32114.8526-0.56850.34330.14790.48070.70970.27091.43650.4578-0.40030.47880.0966-0.1460.6929-0.06970.544517.1251-42.314536.9068
82.63212.13230.97521.9484-0.27337.3325-0.3358-1.33721.30260.35650.3179-0.4383-0.4233-0.01250.37150.34640.2272-0.17980.7318-0.21060.394812.0439-30.225725.2557
94.1712-2.4112-0.18995.85033.76027.0831-0.2826-0.7674-0.36620.54720.05350.08550.305-0.24110.1150.16730.0058-0.00130.34150.1120.240812.0839-48.855818.4876
108.188-2.3034-0.35986.34412.15083.5819-0.04940.1669-0.4533-0.3972-0.0588-0.01620.08740.07660.06760.18540.00960.03920.21150.04480.150113.0691-48.82844.452
113.40554.9751-1.81478.7463-3.1433.1136-0.40280.2803-0.1801-0.47210.2601-0.48880.09620.27810.20820.1204-0.02150.01520.48010.05150.336734.9779-36.89874.4169
124.24570.29010.47214.078-6.2588.459-0.33010.06560.11630.76490.3394-0.2665-0.7535-0.1791-0.00980.1873-0.02410.00240.33480.04980.40931.9712-30.58218.6769
130.32450.2986-1.10270.3306-1.06692.32670.45471.24082.00490.0168-0.5261-1.3237-0.68790.0887-0.09670.51760.01070.03350.55770.12131.197711.2731-18.40494.6483
143.0572-0.6399-1.79640.46740.97982.172-0.0803-0.3822.0166-0.41190.2777-1.8068-0.43350.107-0.04720.3140.1288-0.01960.4085-0.02861.06565.6295-15.994613.1916
153.5294-4.74490.39686.4386-1.10192.8923-0.7165-0.46152.24531.31850.1734-1.2358-0.73580.16330.16030.41560.0614-0.20540.4315-0.38771.345-1.8424-9.725221.1881
164.8644-5.6714-4.4378.62156.90696.0032-0.0428-0.2050.1835-0.1737-0.27250.5032-0.2513-0.33610.17750.24550.0366-0.08680.4037-0.07390.4693-1.4956-23.012513.7494
175.84732.47951.6238.04040.45092.46760.03940.34040.2309-0.5362-0.2577-0.14590.15020.31680.15850.22140.03610.00020.32150.04290.186714.6238-45.6046-2.4244
184.5068-4.6462-1.62518.6776.12934.5817-1.0394-1.0206-0.79930.9047-0.0041.45250.9149-0.31570.36550.29620.05230.09210.55690.11980.27482.8929-52.728318.892
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 78 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 110 )
5X-RAY DIFFRACTION5chain 'A' and (resid 111 through 120 )
6X-RAY DIFFRACTION6chain 'A' and (resid 121 through 134 )
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 30 )
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 47 )
9X-RAY DIFFRACTION9chain 'B' and (resid 48 through 75 )
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 102 )
11X-RAY DIFFRACTION11chain 'C' and (resid 182 through 220 )
12X-RAY DIFFRACTION12chain 'C' and (resid 221 through 242 )
13X-RAY DIFFRACTION13chain 'C' and (resid 243 through 264 )
14X-RAY DIFFRACTION14chain 'C' and (resid 265 through 285 )
15X-RAY DIFFRACTION15chain 'C' and (resid 286 through 305 )
16X-RAY DIFFRACTION16chain 'C' and (resid 306 through 333 )
17X-RAY DIFFRACTION17chain 'C' and (resid 334 through 354 )
18X-RAY DIFFRACTION18chain 'C' and (resid 355 through 386 )

+
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