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- PDB-2jm1: Structures and chemical shift assignments for the ADD domain of t... -

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Basic information

Entry
Database: PDB / ID: 2jm1
TitleStructures and chemical shift assignments for the ADD domain of the ATRX protein
ComponentsTranscriptional regulator ATRX
KeywordsMETAL BINDING PROTEIN / ADD domain
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 / Inhibition of DNA recombination at telomere / forebrain development / methylated histone binding / helicase activity / multicellular organism growth / PML body / chromatin DNA binding / nucleosome assembly / chromatin organization / histone binding / chromosome, telomeric region / spermatogenesis / DNA helicase / transcription by RNA polymerase II / chromatin remodeling / nuclear body / DNA repair / chromatin binding / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / nucleoplasm / ATP binding / 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 / 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 / Helicase conserved C-terminal domain / Zinc finger, FYVE/PHD-type / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsYang, J. / Neuhaus, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Structural consequences of disease-causing mutations in the ATRX-DNMT3-DNMT3L (ADD) domain of the chromatin-associated protein ATRX.
Authors: Argentaro, A. / Yang, J.C. / Chapman, L. / Kowalczyk, M.S. / Gibbons, R.J. / Higgs, D.R. / Neuhaus, D. / Rhodes, D.
History
DepositionSep 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.5May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator ATRX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4144
Polymers16,2181
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)32 / 100lowest 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: 16217.552 Da / Num. of mol.: 1 / Fragment: ADD domain, residues 159-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATRX, RAD54L, XH2 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Rosetta pLysS
References: UniProt: P46100, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: 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 NOESY
1313D 1H-15N NOESY
1413D HNHB
1522D 1H-15N HSQC
1622D 1H-13C HSQC
1723D HN(CA)CB
1823D HN(COCA)CB
1923D HNCA
11023D HN(CO)CA
1112HNHAHB
1122HN(CO)HAHB
11323D (H)CCH-TOCSY
11423D (H)CCH-COSY
11523D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-15N] ADD domain 156-296, 20 mM TRIS, 1 mM DTT, 100 uM zinc chloride, 0.5 M sodium chloride, 93% H2O, 7% D2O93% H2O/7% D2O
20.35 mM [U-13C; U-15N] ADD domain 156-296, 20 mM TRIS, 1 mM DTT, 100 uM zinc chloride, 0.5 M sodium chloride, 93% H2O, 7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMADD domain 156-296[U-15N]1
20 mMTRISnone1
1 mMDTTnone1
100 uMzinc chloridenone1
0.5 Msodium chloridenone1
0.3 mMADD domain 156-296[U-13C; U-15N]2
20 mMTRISnone2
1 mMDTTnone2
100 uMzinc chloridenone2
0.5 Msodium chloridenone2
Sample conditionsIonic strength: 0.5 / pH: 6.7 / Pressure: ambient / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
SparkyT Goddarddata analysis
SparkyT Goddardpeak picking
X-PLOR3.8AT Brungerstructure solution
X-PLOR3.8AT Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy / Conformers calculated total number: 100 / Conformers submitted total number: 32 / Maximum upper distance constraint violation: 0.27 Å

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