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- PDB-2ld1: Structures and chemical shift assignments for the ADD domain of t... -

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Basic information

Entry
Database: PDB / ID: 2ld1
TitleStructures and chemical shift assignments for the ADD domain of the ATRX protein
ComponentsTranscriptional regulator ATRX
KeywordsMETAL BINDING PROTEIN / HYDROLASE
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 / condensed chromosome, centromeric region / protein localization to chromosome, telomeric region / nuclear chromosome / seminiferous tubule development / positive regulation of telomere maintenance / replication fork processing / subtelomeric heterochromatin formation / heterochromatin / pericentric heterochromatin / forebrain development / : / Inhibition of DNA recombination at telomere / DNA damage response, signal transduction by p53 class mediator / PML body / multicellular organism growth / chromatin DNA binding / nucleosome assembly / chromatin organization / spermatogenesis / DNA helicase / histone binding / transcription by RNA polymerase II / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / chromosome, telomeric region / nuclear body / chromatin remodeling / DNA repair / chromatin binding / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / zinc ion binding / nucleoplasm / ATP binding / nucleus
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
Model detailslowest energy, model 1
AuthorsNeuhaus, D. / Yang, J.
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
DepositionMay 13, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4714
Polymers16,2751
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)34 / 100structures 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: ADD DOMAIN, 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) / Strain (production host): BL21 DE3 ROSETTA PLYSS / References: UniProt: P46100, DNA helicase
#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 1H-1H 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
11123D HNHAHB
11223D HN(CO)HAHB
11323D (H)CCH-TOCSY
11423D (H)CCH-COSY
11523D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6-0.8 mM [U-15N] ADD_domain_163-296, 20 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 100 uM zinc chloride, 0.5 M sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
20.3-0.4 mM [U-13C; U-15N] ADD_domain_163-296, 20 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 100 uM zinc chloride, 0.5 M sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMADD_domain_163-296-1[U-15N]0.6-0.81
20 mMTRIS-2[U-2H]1
1 mMDTT-3[U-2H]1
100 uMzinc chloride-41
0.5 Msodium chloride-51
mMADD_domain_163-296-6[U-13C; U-15N]0.3-0.42
20 mMTRIS-7[U-2H]2
1 mMDTT-8[U-2H]2
100 uMzinc chloride-92
0.5 Msodium chloride-102
Sample conditionsIonic strength: 0.5 / pH: 6.7 / Pressure: ambient / Temperature: 300 K

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NMR measurement

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
SparkyGoddarddata analysis
SparkyGoddardpeak picking
X-PLOR3.8Brungerstructure solution
X-PLOR3.8Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1423 / NOE intraresidue total count: 500 / NOE long range total count: 351 / NOE medium range total count: 231 / NOE sequential total count: 341 / Hydrogen bond constraints total count: 38 / 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: 100 / Conformers submitted total number: 34 / Maximum upper distance constraint violation: 0.33 Å

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