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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, subtelomeric region / chromosome organization involved in meiotic cell cycle / Sertoli cell development / cellular response to hydroxyurea / meiotic spindle organization ...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, subtelomeric region / chromosome organization involved in meiotic cell cycle / Sertoli cell development / cellular response to hydroxyurea / meiotic spindle organization / chromo shadow domain binding / DNA translocase activity / seminiferous tubule development / condensed chromosome, centromeric region / histone H3K9me2/3 reader activity / protein localization to chromosome, telomeric region / nuclear chromosome / forebrain development / : / positive regulation of telomere maintenance / replication fork processing / pericentric heterochromatin / subtelomeric heterochromatin formation / heterochromatin / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / 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 / epigenetic regulation of gene expression / 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 / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / DNA damage response, signal transduction by p53 class mediator / RNA Polymerase I Promoter Escape / chromatin DNA binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / helicase activity / 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 / PML body / 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 / multicellular organism growth / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nucleosome assembly / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / 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 / Oxidative Stress Induced Senescence / spermatogenesis / histone binding / DNA helicase / gene expression / Estrogen-dependent gene expression / transcription by RNA polymerase II / chromosome, telomeric region / nuclear body / chromatin remodeling / cadherin binding / 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 / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / ATP binding / nucleus / membrane
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 / 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
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _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: 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
Has protein modificationY

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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 / 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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