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- PDB-5grq: Crystal Structure of DHB domain of Daxx in complex with an ATRX p... -

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Basic information

Entry
Database: PDB / ID: 5grq
TitleCrystal Structure of DHB domain of Daxx in complex with an ATRX peptide
Components
  • Death domain-associated protein 6
  • Transcriptional regulator ATRX
KeywordsHYDROLASE / helical bundle protein
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 / 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, subtelomeric region / cellular response to sodium arsenite / chromosome organization involved in meiotic cell cycle ...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 / 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, subtelomeric region / cellular response to sodium arsenite / 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 / cellular response to cadmium ion / nuclear androgen receptor binding / nuclear chromosome / positive regulation of telomere maintenance / replication fork processing / pericentric heterochromatin / androgen receptor signaling pathway / protein kinase activator activity / extrinsic apoptotic signaling pathway via death domain receptors / chromosome, centromeric region / regulation of protein ubiquitination / : / cellular response to unfolded protein / forebrain development / subtelomeric heterochromatin formation / heterochromatin / transcription regulator inhibitor activity / cellular response to copper ion / JNK cascade / heat shock protein binding / Inhibition of DNA recombination at telomere / SUMOylation of transcription cofactors / DNA damage response, signal transduction by p53 class mediator / chromatin DNA binding / molecular condensate scaffold activity / helicase activity / PML body / multicellular organism growth / HCMV Early Events / Regulation of TP53 Degradation / transcription corepressor activity / p53 binding / nucleosome assembly / regulation of gene expression / chromatin organization / cellular response to heat / histone binding / spermatogenesis / regulation of apoptotic process / DNA helicase / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / chromosome, telomeric region / nuclear body / chromatin remodeling / negative regulation of gene expression / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / regulation of DNA-templated transcription / protein kinase binding / nucleolus / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Daxx helical bundle domain / 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 ...Daxx helical bundle domain / 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, Ruva Protein; domain 3 / Zinc finger, FYVE/PHD-type / Helicase conserved C-terminal domain / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Transcriptional regulator ATRX / Death domain-associated protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.584 Å
AuthorsLi, H.
CitationJournal: To be published
Title: Crystal Structure of DHB domain of Daxx in complex with an ATRX peptide
Authors: Li, H.
History
DepositionAug 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 2.0Oct 18, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / audit_author ...atom_site / audit_author / citation_author / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq
Item: _atom_site.label_entity_id / _struct_ref_seq.db_align_end ..._atom_site.label_entity_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end
Revision 2.1Mar 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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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: Death domain-associated protein 6
C: Transcriptional regulator ATRX
D: Transcriptional regulator ATRX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,16525
Polymers27,9164
Non-polymers1,24921
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-421 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.428, 56.217, 102.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 10537.360 Da / Num. of mol.: 2 / Fragment: DHB domain, UNP residues 55-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAXX, BING2, DAP6 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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: 3420.712 Da / Num. of mol.: 2 / Fragment: DID domain, UNP residues 1256-1285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATRX, RAD54L, XH2 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P46100, DNA helicase

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Non-polymers , 5 types, 429 molecules

#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.79 Å3/Da / Density % sol: 55.93 % / Mosaicity: 0.311 °
Preparation: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 100mM MES 6.0, 100mM zinc acetate, 13% ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: PSI PILATUS 6M / Detector: AREA DETECTOR / Date: Sep 5, 2015 / Details: PSI PILATUS 6M
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 80904 / % possible obs: 99.5 % / Redundancy: 12.8 % / Biso Wilson estimate: 12.99 Å2 / Rmerge(I) obs: 0.076 / Net I/av σ(I): 32.714 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.58-1.6110.40.5150.926190.5
1.61-1.6412.80.4890.9591100
1.64-1.6713.20.4340.973199.9
1.67-1.713.10.3820.9731100
1.7-1.7413.20.3620.976199.9
1.74-1.7812.70.30.9781100
1.78-1.8211.90.2590.98199.9
1.82-1.8713.20.2280.9871100
1.87-1.9313.30.2760.9661100
1.93-1.9913.40.1670.9921100
1.99-2.0613.10.1380.9931100
2.06-2.1412.50.1380.988199.9
2.14-2.2412.30.0930.9951100
2.24-2.3613.40.1060.9891100
2.36-2.5113.40.0680.9981100
2.51-2.713.10.0640.9981100
2.7-2.9712.50.0510.9981100
2.97-3.413.50.0450.9991100
3.4-4.2912.30.0430.998199.9
4.29-5012.40.040.998199.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2689: ???)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.584→49.336 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 16.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1789 3970 4.91 %
Rwork0.1575 --
obs0.1585 80895 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.584→49.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 41 408 2331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061930
X-RAY DIFFRACTIONf_angle_d0.7862585
X-RAY DIFFRACTIONf_dihedral_angle_d11.6751205
X-RAY DIFFRACTIONf_chiral_restr0.043285
X-RAY DIFFRACTIONf_plane_restr0.005339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5836-1.60290.174960.172517X-RAY DIFFRACTION90
1.6029-1.62320.16751220.16522756X-RAY DIFFRACTION99
1.6232-1.64460.16681530.15622742X-RAY DIFFRACTION100
1.6446-1.66710.20471230.16222812X-RAY DIFFRACTION100
1.6671-1.69090.1811660.1572732X-RAY DIFFRACTION100
1.6909-1.71620.16071530.15812790X-RAY DIFFRACTION100
1.7162-1.7430.16531060.16772789X-RAY DIFFRACTION100
1.743-1.77150.19181620.16082739X-RAY DIFFRACTION100
1.7715-1.80210.1965990.16232824X-RAY DIFFRACTION100
1.8021-1.83490.16341520.15952749X-RAY DIFFRACTION100
1.8349-1.87020.19761510.16422745X-RAY DIFFRACTION100
1.8702-1.90830.26581670.19022696X-RAY DIFFRACTION98
1.9083-1.94980.32571350.25742689X-RAY DIFFRACTION97
1.9498-1.99520.21781270.16322755X-RAY DIFFRACTION100
1.9952-2.04510.16651800.14442757X-RAY DIFFRACTION100
2.0451-2.10040.25121630.21182680X-RAY DIFFRACTION99
2.1004-2.16220.17931220.15252798X-RAY DIFFRACTION100
2.1622-2.2320.1621470.14812772X-RAY DIFFRACTION100
2.232-2.31170.18171330.18472709X-RAY DIFFRACTION98
2.3117-2.40430.1411570.14312772X-RAY DIFFRACTION100
2.4043-2.51370.17531430.14532772X-RAY DIFFRACTION100
2.5137-2.64620.16991290.15072781X-RAY DIFFRACTION100
2.6462-2.8120.18491300.14942776X-RAY DIFFRACTION100
2.812-3.02910.14631660.14572723X-RAY DIFFRACTION100
3.0291-3.33390.16881560.1372776X-RAY DIFFRACTION100
3.3339-3.81620.15771580.1342744X-RAY DIFFRACTION100
3.8162-4.80730.15461260.13482786X-RAY DIFFRACTION100
4.8073-49.36040.18261480.1732744X-RAY DIFFRACTION99
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)
12.63091.7123-1.92472.9094-0.06113.7869-0.144-0.0087-0.07350.2364-0.07310.21320.2167-0.2210.22040.137-0.00150.02410.1169-0.02120.115858.8071-21.426272.3748
21.29860.0789-2.81220.3718-0.36226.1188-0.0738-0.0719-0.1263-0.044-0.0599-0.09780.02520.20350.16370.09290.00260.00380.13560.01630.128569.9931-18.034257.724
30.99910.2694-0.83230.4998-0.51431.0792-0.03050.0531-0.0248-0.0140.0182-0.05350.01290.00780.01020.0979-0.0018-0.00770.10340.00220.093663.4865-15.298755.7048
41.6855-1.0202-1.58461.44530.9733.1285-0.04570.1959-0.0347-0.15120.0373-0.06630.0415-0.2034-0.09320.1002-0.02890.01120.1147-0.00980.107159.5753-16.161350.103
53.4092.8807-4.58564.4374-4.71876.55060.36050.20520.65090.13790.2788-0.3949-0.93310.4735-0.23010.3947-0.0540.08350.2287-0.03030.325260.31011.026257.8806
60.67240.28660.57071.0781.73133.94940.01250.01210.0298-0.0591-0.04270.0084-0.0747-0.05930.05340.1119-0.0026-0.0020.07930.00250.106454.2665-2.666481.9511
70.92340.1513-0.05321.51491.28312.4894-0.05560.13090.0183-0.02530.09-0.06430.01770.1676-0.00280.1195-0.0122-0.03150.1340.00510.13364.2813-4.516891.8141
84.4841-0.9636-0.68145.0804-0.30613.1466-0.0661-0.1340.0738-0.02190.0461-0.13010.02320.22730.00260.1085-0.00460.01070.088-0.0080.067560.2978-13.262977.4685
90.3747-0.35720.08351.24290.12281.88340.0115-0.0027-0.06920.084-0.0380.06620.108-0.02460.03110.1104-0.01620.01380.0870.00440.118752.6212-10.244890.0452
103.79390.1816-2.48752.2713-1.71076.2496-0.11460.3684-0.1177-0.113-0.10390.12240.5487-0.66740.23640.237-0.03140.01770.252-0.03930.18768.0037-18.571631.7812
111.70350.27260.04125.58972.21583.27130.03280.2690.0505-0.255-0.09030.3586-0.2136-0.50660.01090.1347-0.0004-0.00290.2160.02270.145660.0497-9.530742.0902
122.1965-1.16750.31995.3177-1.07191.0269-0.2565-0.30810.4870.54350.0516-0.1337-0.2188-0.07910.18920.54760.11390.06890.69130.08070.413952.1873-4.6714109.1359
135.53320.5487-0.97062.4888-0.15522.15120.0381-0.3057-0.4420.2618-0.0966-0.10740.17410.32490.04240.19130.0032-0.03370.17490.05960.155362.4122-12.2912101.1426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 55 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 119 )
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 137 )
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 144 )
6X-RAY DIFFRACTION6chain 'B' and (resid 55 through 77 )
7X-RAY DIFFRACTION7chain 'B' and (resid 78 through 93 )
8X-RAY DIFFRACTION8chain 'B' and (resid 94 through 102 )
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 139 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1256 through 1266 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1267 through 1285 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1259 through 1266 )
13X-RAY DIFFRACTION13chain 'D' and (resid 1267 through 1284 )

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