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- PDB-2lbm: Solution structure of the ADD domain of ATRX complexed with histo... -

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Basic information

Entry
Database: PDB / ID: 2lbm
TitleSolution structure of the ADD domain of ATRX complexed with histone tail H3 1-15 K9me3
Components
  • Transcriptional regulator ATRX
  • histone tail H3 K9me3
KeywordsMETAL BINDING PROTEIN/STRUCTURAL PROTEIN / histone tail / METAL BINDING PROTEIN-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 / positive regulation of nuclear cell cycle DNA replication / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / chromosome organization involved in meiotic cell cycle / chromosome, subtelomeric region / Sertoli cell development / meiotic spindle organization / cellular response to hydroxyurea ...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 / positive regulation of nuclear cell cycle DNA replication / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / chromosome organization involved in meiotic cell cycle / chromosome, subtelomeric region / Sertoli cell development / meiotic spindle organization / cellular response to hydroxyurea / DNA translocase activity / chromo shadow domain binding / positive regulation of telomere maintenance / condensed chromosome, centromeric region / ATP-dependent chromatin remodeler activity / protein localization to chromosome, telomeric region / nuclear chromosome / seminiferous tubule development / replication fork processing / DNA damage response, signal transduction by p53 class mediator / subtelomeric heterochromatin formation / heterochromatin / pericentric heterochromatin / Chromatin modifying enzymes / epigenetic regulation of gene expression / forebrain development / Inhibition of DNA recombination at telomere / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / helicase activity / DNA methylation / Condensation of Prophase Chromosomes / 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 / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / multicellular organism growth / chromatin DNA binding / PKMTs methylate histone lysines / PML body / Meiotic recombination / RMTs methylate histone arginines / 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 / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / Oxidative Stress Induced Senescence / DNA helicase / Estrogen-dependent gene expression / transcription by RNA polymerase II / chromosome, telomeric region / nuclear body / chromatin remodeling / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / DNA repair / chromatin binding / regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding
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 / Histone H3 signature 1. / Helicase conserved C-terminal domain ...ATRX, ADD domain / Cysteine Rich ADD domain / ADD domain / ADD domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Histone H3 signature 1. / Helicase conserved C-terminal domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / 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 H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEustermann, S. / Yang, J. / Neuhaus, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin
Authors: Eustermann, S. / Yang, J. / Law, M.J. / Amos, R. / Chapman, L.M. / Jelinska, C. / Garrick, D. / Clynes, D. / Gibbons, R.J. / Rhodes, D. / Higgs, D.R. / Neuhaus, D.
History
DepositionApr 8, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator ATRX
C: histone tail H3 K9me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0795
Polymers17,8822
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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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: 16274.603 Da / Num. of mol.: 1 / Fragment: UNP residues 159-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATRX, RAD54L, XH2 / Production host: Escherichia coli (E. coli) / References: UniProt: P46100, DNA helicase
#2: Protein/peptide histone tail H3 K9me3


Mass: 1607.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aliphatic (constant-time)
1412D 1H-13C HSQC aromatic (constant-time)
1522D 1H-1H NOESY (13C-H rejected in F1 and F2)
1613D HNCA
1713D HN(CO)CA
1813D HBHA(CO)NH
1913D (H)CCH-TOCSY
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic
11422D 1H-1H TOCSY (13C-H rejected in F1 and F2)
11512D 1H-1H NOESY (15N-H rejected in F2)
11623D 1H-13C NOESY aliphatic
11723D 1H-13C NOESY aromatic
11823D 1H-13C NOESY aliphatic (rejected 13C-H in F1, 12C-H in F3)
11922D 1H-1H NOESY (13C-H rejected F1, 12C-H rejected F2)
12012D 1H-1H NOESY (13C-H and 15N-H rejected in F1 and F2)

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Sample preparation

Details
Solution-IDContentsSolvent system
1200 uM [U-98% 13C; U-98% 15N] ATRX ADD domain-1, 200 uM H3 tail 1-15 K9me3-2, 50 mM [U-99% 2H] TRIS-3, 200 mM sodium chloride-4, 150 uM zinc sulfate-5, 1 mM [U-99% 2H] DTT-6, 95% H2O/5% D2O95% H2O/5% D2O
2200 uM [U-98% 13C; U-98% 15N] ATRX ADD domain-7, 200 uM H3 tail 1-15 K9me3-8, 50 mM [U-99% 2H] TRIS-9, 200 mM sodium chloride-10, 150 uM zinc sulfate-11, 1 mM [U-99% 2H] DTT-12, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMATRX ADD domain-1[U-98% 13C; U-98% 15N]1
200 uMH3 tail 1-15 K9me3-21
50 mMTRIS-3[U-99% 2H]1
200 mMsodium chloride-41
150 uMzinc sulfate-51
1 mMDTT-6[U-99% 2H]1
200 uMATRX ADD domain-7[U-98% 13C; U-98% 15N]2
200 uMH3 tail 1-15 K9me3-82
50 mMTRIS-9[U-99% 2H]2
200 mMsodium chloride-102
150 uMzinc sulfate-112
1 mMDTT-12[U-99% 2H]2
Sample conditionsIonic strength: 250 / pH: 7.0 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Bruker DMXBrukerDMX6002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameVersionDeveloperClassification
xplor-nih2.19Schwieters, Kuszewski, Tjandra and Clorestructure solution
sparkyGoddardchemical shift assignment
TOPSPIN2.1Bruker Biospinprocessing
xplor-nihrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1582 / NOE intraresidue total count: 497 / NOE long range total count: 377 / NOE medium range total count: 312 / NOE sequential total count: 339 / Hydrogen bond constraints total count: 40 / Protein chi angle constraints total count: 30 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 0 / Protein psi angle constraints total count: 0
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25 / Maximum torsion angle constraint violation: 5.19 ° / Maximum upper distance constraint violation: 0.31 Å / Representative conformer: 1

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