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- PDB-3qln: Crystal structure of ATRX ADD domain in free state -

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Basic information

Entry
Database: PDB / ID: 3qln
TitleCrystal structure of ATRX ADD domain in free state
ComponentsTranscriptional regulator ATRX
KeywordsTRANSCRIPTION / zinc finger / histone tail / lysine methylation / nuclear protein
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å
AuthorsLi, H. / Patel, D.J.
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 3, 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 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Assembly

Deposited unit
A: Transcriptional regulator ATRX
B: Transcriptional regulator ATRX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9808
Polymers29,5882
Non-polymers3926
Water6,017334
1
A: Transcriptional regulator ATRX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9904
Polymers14,7941
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcriptional regulator ATRX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9904
Polymers14,7941
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.167, 74.167, 54.091
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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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.: 2 / 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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.9 Å3/Da / Density % sol: 57.63 % / Mosaicity: 0.461 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% (v/v) PEG 4000, 100mM HEPES-NaOH, 0.2M KCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.2827 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2827 Å / Relative weight: 1
ReflectionRedundancy: 11.2 % / Number: 292020 / Rmerge(I) obs: 0.08 / Χ2: 3.22 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 26178 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.165099.210.0648.77311.6
4.095.1610010.0555.40111
3.584.0910010.0574.92810.9
3.253.5810010.0655.24610.9
3.023.2510010.0745.0611
2.843.0210010.0824.19411.2
2.72.8410010.0883.67911.3
2.582.710010.0983.14611.2
2.482.5810010.1142.86411.3
2.392.4810010.1242.61511.2
2.322.3910010.1422.32811.3
2.252.3210010.1732.17611.2
2.192.2510010.192.20311.2
2.142.1910010.2081.91411.2
2.092.1410010.251.79411.2
2.052.0910010.2991.82411.1
2.012.0510010.3471.59711.1
1.972.0110010.4291.45911.1
1.931.9710010.5571.46511.1
1.91.9310010.5821.5411
Reflection twinOperator: -h,-k,l / Fraction: 0.408
ReflectionResolution: 1.9→50 Å / Num. obs: 52327 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 43.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
CNSphasing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.901→32.115 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8336 / σ(F): 2.13 / Stereochemistry target values: TWIN_LSQ_F
Details: THE FRIEDEL PAIRS WERE USED IN SAD PHASING. DURING REFINEMENT, FRIEDEL PAIRS WERE MERGED.
RfactorNum. reflection% reflection
Rfree0.1583 1997 7.63 %
Rwork0.1271 --
obs0.1298 26159 99.97 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.109 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 117.44 Å2 / Biso mean: 35.8735 Å2 / Biso min: 19.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.8899 Å20 Å20 Å2
2---0.8899 Å2-0 Å2
3---1.7799 Å2
Refinement stepCycle: LAST / Resolution: 1.901→32.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 6 334 2275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061975
X-RAY DIFFRACTIONf_angle_d0.9192667
X-RAY DIFFRACTIONf_chiral_restr0.065281
X-RAY DIFFRACTIONf_plane_restr0.004351
X-RAY DIFFRACTIONf_dihedral_angle_d15.722730
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9015-1.9490.21971500.21621717186792
1.949-2.00160.20951380.19381733187193
2.0016-2.06030.22931480.18141699184792
2.0603-2.12670.17421460.17271707185392
2.1267-2.20250.17451380.16741714185293
2.2025-2.29040.19231400.17381748188893
2.2904-2.39430.18751450.16961722186792
2.3943-2.52010.18011410.15991711185292
2.5201-2.67730.20391440.15691746189092
2.6773-2.88280.17491360.13731698183493
2.8828-3.17080.1721490.12481733188292
3.1708-3.62470.13331390.10441716185593
3.6247-4.54830.11351390.08031725186493
4.5483-15.72250.1361440.10071728187292

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