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- PDB-5y18: Crystal structure of DAXX helical bundle domain in complex with ATRX -

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Basic information

Entry
Database: PDB / ID: 5y18
TitleCrystal structure of DAXX helical bundle domain in complex with ATRX
Components
  • Death domain-associated protein 6
  • Transcriptional regulator ATRX
KeywordsPROTEIN BINDING / chromatin remodeling / histone chaperone
Function / homology
Function and homology information


post-embryonic forelimb morphogenesis / cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / SUMO-modified protein reader activity / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / 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 ...post-embryonic forelimb morphogenesis / cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / SUMO-modified protein reader activity / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / 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 / cellular response to sodium arsenite / 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 / transcription regulator inhibitor activity / ATP-dependent chromatin remodeler activity / protein localization to chromosome, telomeric region / nuclear androgen receptor binding / nuclear chromosome / seminiferous tubule development / replication fork processing / protein kinase activator activity / androgen receptor signaling pathway / chromosome, centromeric region / regulation of protein ubiquitination / DNA damage response, signal transduction by p53 class mediator / extrinsic apoptotic signaling pathway via death domain receptors / subtelomeric heterochromatin formation / positive regulation of protein kinase activity / cellular response to unfolded protein / heterochromatin / pericentric heterochromatin / JNK cascade / forebrain development / cellular response to copper ion / Inhibition of DNA recombination at telomere / heat shock protein binding / methylated histone binding / cellular response to cadmium ion / helicase activity / SUMOylation of transcription cofactors / molecular condensate scaffold activity / multicellular organism growth / chromatin DNA binding / PML body / HCMV Early Events / transcription corepressor activity / nucleosome assembly / Regulation of TP53 Degradation / p53 binding / chromatin organization / cellular response to heat / histone binding / spermatogenesis / regulation of gene expression / regulation of apoptotic process / DNA helicase / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / chromosome, telomeric region / transcription coactivator activity / nuclear body / chromatin remodeling / positive regulation of protein phosphorylation / negative regulation of gene expression / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / regulation of DNA-templated transcription / nucleolus / protein kinase binding / enzyme binding / protein homodimerization activity / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
ATRX, ADD domain / Cysteine Rich ADD domain / Daxx, N-terminal Rassf1C-interacting domain / Daxx, N-terminal domain superfamily / Daxx, histone-binding domain / Daxx, histone-binding domain superfamily / Daxx N-terminal Rassf1C-interacting domain / Death domain-associated protein 6, histone binding domain / ADD domain / ADD domain profile. ...ATRX, ADD domain / Cysteine Rich ADD domain / Daxx, N-terminal Rassf1C-interacting domain / Daxx, N-terminal domain superfamily / Daxx, histone-binding domain / Daxx, histone-binding domain superfamily / Daxx N-terminal Rassf1C-interacting domain / Death domain-associated protein 6, histone binding 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 / Death domain-associated protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.202 Å
AuthorsChen, Y. / Wang, X.
CitationJournal: Protein Cell / Year: 2017
Title: Structural basis for DAXX interaction with ATRX
Authors: Wang, X. / Zhao, Y. / Zhang, J. / Chen, Y.
History
DepositionJul 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Death domain-associated protein 6
B: Transcriptional regulator ATRX


Theoretical massNumber of molelcules
Total (without water)13,6812
Polymers13,6812
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, A,B forms a heterodimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-8 kcal/mol
Surface area6200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.485, 107.904, 30.887
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Death domain-associated protein 6 / Daxx / hDaxx / ETS1-associated protein 1 / EAP1 / Fas death domain-associated protein


Mass: 10995.709 Da / Num. of mol.: 1 / Fragment: UNP residues 55-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAXX, BING2, DAP6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UER7
#2: Protein/peptide Transcriptional regulator ATRX / ATP-dependent helicase ATRX / X-linked helicase II / X-linked nuclear protein / XNP / Znf-HX


Mass: 2684.854 Da / Num. of mol.: 1 / Fragment: UNP residues 1268-1289
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAuthors state that the extra residue S is a remained residue after cleavage of fusion tag.

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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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M sodium citrate, pH6.5, 0.2M ammonium acetate, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 6179 / % possible obs: 99.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.033 / Rrim(I) all: 0.084 / Χ2: 0.851 / Net I/σ(I): 6.6 / Num. measured all: 38355
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.285.40.4135940.9010.1920.4570.95799.8
2.28-2.376.10.3036150.950.1320.3321.00499.5
2.37-2.486.50.2565890.9570.1080.2790.991100
2.48-2.616.50.196100.9750.080.2060.9799.7
2.61-2.776.20.1536060.9820.0660.1670.92799.3
2.77-2.996.40.1226160.9880.0510.1320.853100
2.99-3.296.50.0846160.990.0360.0910.72699.8
3.29-3.766.20.0566270.9970.0240.0610.7198.9
3.76-4.746.50.0446290.9970.0190.0480.64899.8
4.74-505.80.0536770.9950.0240.0580.77198.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data collection
HKL-3000data scaling
SHARPphasing
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.202→26.976 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 21.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2192 311 5.06 %
Rwork0.1865 5831 -
obs0.188 6142 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.66 Å2 / Biso mean: 37.305 Å2 / Biso min: 19.93 Å2
Refinement stepCycle: final / Resolution: 2.202→26.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 0 52 866
Biso mean---45.32 -
Num. residues----102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002827
X-RAY DIFFRACTIONf_angle_d0.531109
X-RAY DIFFRACTIONf_chiral_restr0.02127
X-RAY DIFFRACTIONf_plane_restr0.002138
X-RAY DIFFRACTIONf_dihedral_angle_d13.787314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2024-2.77430.26321480.206728432991
2.7743-26.9780.20241630.179129883151
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6475-1.9783-2.02857.92415.09863.8255-0.18180.02020.16870.02060.1498-0.1314-0.120.12780.01720.3184-0.01120.01680.31090.10240.336526.33125.06280.9797
21.75650.6517-0.71524.6033.02183.0934-0.09250.2594-0.2453-0.24440.0980.00140.1698-0.65070.17470.3255-0.01160.03760.33440.020.295916.890918.29170.1513
38.8208-5.4433-5.92397.08555.74365.1491-0.4343-0.2436-0.08440.27190.39210.07860.45130.31930.07390.294-0.0049-0.00390.29510.01180.248630.846718.05195.8071
48.686-1.5041-4.30384.0522.62366.3965-0.27510.0724-1.1444-0.01220.09730.2732-0.0622-0.11570.15550.3317-0.0570.06770.22730.01370.3721.870812.41913.4963
52.2715-3.34541.79456.3317-0.30425.3112-0.2119-0.2672-1.03730.03330.62260.4950.6331-0.5295-0.29020.4126-0.10420.07840.2896-0.01820.562720.084.0052-3.7211
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 77 )A56 - 77
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 102 )A78 - 102
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 119 )A103 - 119
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 140 )A120 - 140
5X-RAY DIFFRACTION5chain 'B' and (resid 1267 through 1283 )B0

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