[English] 日本語
Yorodumi
- PDB-4h9q: Complex structure 4 of DAXX(E225A)/H3.3(sub5)/H4 -

+
Open data


ID or keywords:

Loading...

-
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 / : / 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 / spermatid development / protein kinase activator activity / regulation of protein ubiquitination / 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 / 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 / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / SUMOylation of transcription cofactors / 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 / G2/M DNA damage checkpoint / PML body / 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 / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / male gonad development / Transcriptional regulation of granulopoiesis / HCMV Early Events / osteoblast differentiation / structural constituent of chromatin / p53 binding / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / cellular response to heat / 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 / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth
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: 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

-
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)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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
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