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- PDB-3ql9: Monoclinic complex structure of ATRX ADD bound to histone H3K9me3... -

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Basic information

Entry
Database: PDB / ID: 3ql9
TitleMonoclinic complex structure of ATRX ADD bound to histone H3K9me3 peptide
Components
  • Transcriptional regulator ATRX
  • peptide of Histone H3.3
KeywordsTRANSCRIPTION/STRUCTURAL PROTEIN / zinc finger / transcription / histone / lysine trimethylation / nuclear protein / HISTONE-BINDING PROTEIN / TRANSCRIPTION-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


post-embryonic forelimb morphogenesis / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / positive regulation of nuclear cell cycle DNA replication / chromosome, subtelomeric region / chromosome organization involved in meiotic cell cycle / negative regulation of chromosome condensation / Sertoli cell development / Barr body ...post-embryonic forelimb morphogenesis / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / positive regulation of nuclear cell cycle DNA replication / chromosome, subtelomeric region / chromosome organization involved in meiotic cell cycle / negative regulation of chromosome condensation / Sertoli cell development / Barr body / : / cellular response to hydroxyurea / chromo shadow domain binding / DNA translocase activity / meiotic spindle organization / condensed chromosome, centromeric region / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / histone H3K9me2/3 reader activity / oocyte maturation / nucleosomal DNA binding / protein localization to chromosome, telomeric region / nuclear chromosome / seminiferous tubule development / nucleus organization / : / forebrain development / positive regulation of telomere maintenance / replication fork processing / spermatid development / single fertilization / subtelomeric heterochromatin formation / RNA polymerase II core promoter sequence-specific DNA binding / pericentric heterochromatin / heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / embryo implantation / telomere organization / 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 / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / 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 / DNA damage response, signal transduction by p53 class mediator / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / helicase 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 / PML body / NoRC negatively regulates rRNA expression / chromatin DNA binding / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / multicellular organism growth / male gonad development / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / osteoblast differentiation / structural constituent of chromatin / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / 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 / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / histone binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / DNA helicase / transcription by RNA polymerase II / chromosome, telomeric region / cell population proliferation / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / DNA repair / chromatin binding / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / extracellular exosome / extracellular region
Similarity search - Function
ATRX, ADD domain / : / Cysteine Rich ADD domain / ADD domain / ADD domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Zinc finger, FYVE/PHD-type ...ATRX, ADD domain / : / Cysteine Rich ADD domain / ADD domain / ADD domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Zinc finger, FYVE/PHD-type / Helicase conserved C-terminal 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 domain / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transcriptional regulator ATRX / Histone H3.3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.93 Å
AuthorsXiang, B. / Li, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome
Authors: Iwase, S. / Xiang, B. / Ghosh, S. / Ren, T. / Lewis, P.W. / Cochrane, J.C. / Allis, C.D. / Picketts, D.J. / Patel, D.J. / Li, H. / Shi, Y.
History
DepositionFeb 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Transcriptional regulator ATRX
C: peptide of Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5985
Polymers16,4022
Non-polymers1963
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-4 kcal/mol
Surface area7580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.719, 39.452, 41.057
Angle α, β, γ (deg.)90.000, 111.240, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-327-

HOH

21A-353-

HOH

31A-355-

HOH

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Components

#1: Protein Transcriptional regulator ATRX / ATP-dependent helicase ATRX / X-linked helicase II / X-linked nuclear protein / XNP / Znf-HX


Mass: 14793.869 Da / Num. of mol.: 1 / Fragment: N-terminal ADD domain, UNP residues 167-289 / Mutation: K251R, F284Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATRX, RAD54L, XH2 / Plasmid: pGEX6p / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: P46100, DNA helicase
#2: Protein/peptide peptide of Histone H3.3


Mass: 1607.877 Da / Num. of mol.: 1
Fragment: K9 trimethylated H3 N-terminal fragment, UNP residues 2-16
Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 1.93 Å3/Da / Density % sol: 36.15 % / Mosaicity: 0.129 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 14% PEG 4000, 0.1M MES, 0.2 M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.97924 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 2, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 0.93→50 Å / Num. obs: 77964 / % possible obs: 93.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Rmerge(I) obs: 0.067 / Χ2: 1.08 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
0.93-0.958.20.5736511.093188.1
0.95-0.968.50.43537091.313188.2
0.96-0.988.50.33736911.174188.8
0.98-18.50.2537171.117189.3
1-1.028.50.20237390.906190.1
1.02-1.058.50.16437760.907190.3
1.05-1.078.60.14337990.845191.3
1.07-1.18.50.12638180.82191.4
1.1-1.148.50.11738100.819192
1.14-1.178.50.10838740.809192.4
1.17-1.218.60.10439280.836193.3
1.21-1.268.60.10138740.863193.8
1.26-1.328.60.09739960.897194.3
1.32-1.398.60.0939230.935194.9
1.39-1.488.60.08240081.064195.5
1.48-1.598.60.0740491.123196.1
1.59-1.758.60.06240501.255196.9
1.75-28.60.05541151.432197.6
2-2.528.60.04641681.548198.3
2.52-508.40.03742691.731198.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QLN

3qln


Resolution: 0.93→21.95 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.9504 / SU ML: 0.1 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1311 3831 5 %Random
Rwork0.1223 ---
all0.1227 83755 --
obs0.1227 76594 91.45 %-
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.962 Å2 / ksol: 0.6 e/Å3
Displacement parametersBiso max: 62.95 Å2 / Biso mean: 9.9856 Å2 / Biso min: 2.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.6165 Å2-0 Å20.5404 Å2
2--0.9324 Å20 Å2
3----0.3159 Å2
Refinement stepCycle: LAST / Resolution: 0.93→21.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1083 0 3 240 1326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021102
X-RAY DIFFRACTIONf_angle_d1.4141485
X-RAY DIFFRACTIONf_chiral_restr0.099157
X-RAY DIFFRACTIONf_plane_restr0.008194
X-RAY DIFFRACTIONf_dihedral_angle_d13.088418
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.9299-0.94170.32111230.35642383250681
0.9417-0.95410.25091190.28672404252383
0.9541-0.96710.23851430.22142495263885
0.9671-0.9810.18291250.17572496262185
0.981-0.99560.14311460.13632529267587
0.9956-1.01120.1341380.12422544268287
1.0112-1.02770.12621380.11092567270588
1.0277-1.04550.11191450.10242556270188
1.0455-1.06450.11721420.09892656279890
1.0645-1.08490.11921510.10142609276090
1.0849-1.10710.11521410.10492671281290
1.1071-1.13120.14051370.1092696283392
1.1312-1.15750.11451610.10482680284192
1.1575-1.18640.10981150.11162726284192
1.1864-1.21850.12121480.10512672282092
1.2185-1.25430.11041420.10462748289093
1.2543-1.29480.11781550.10492745290093
1.2948-1.34110.10271310.10322762289394
1.3411-1.39480.11281250.10322799292494
1.3948-1.45830.10941310.10292815294695
1.4583-1.53510.11041470.09972816296395
1.5351-1.63130.13171540.09892820297496
1.6313-1.75720.11111500.10782840299096
1.7572-1.93390.12441510.11192885303697
1.9339-2.21350.10871670.11222906307398
2.2135-2.78790.12141340.12412940307498
2.7879-21.95630.17061720.15843003317599

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