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- PDB-6f5f: Structure of ARTD2/PARP2 WGR domain bound to double strand DNA wi... -

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Basic information

Entry
Database: PDB / ID: 6f5f
TitleStructure of ARTD2/PARP2 WGR domain bound to double strand DNA with 5 nucleotide overhang and 5'phosphate
Components
  • DNA (5'-D(P*CP*GP*GP*TP*CP*GP*CP*CP*TP*AP*TP*AP*GP*GP*C)-3')
  • Poly [ADP-ribose] polymerase 2
KeywordsDNA BINDING PROTEIN / ADP-ribosylation / DNA repair / DNA end joining / ARTD2 / non-phosphorylated DNA
Function / homology
Function and homology information


response to oxygen-glucose deprivation / hippocampal neuron apoptotic process / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / poly-ADP-D-ribose modification-dependent protein binding / HDR through MMEJ (alt-NHEJ) / NAD+ ADP-ribosyltransferase ...response to oxygen-glucose deprivation / hippocampal neuron apoptotic process / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / poly-ADP-D-ribose modification-dependent protein binding / HDR through MMEJ (alt-NHEJ) / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA repair-dependent chromatin remodeling / NAD+-protein mono-ADP-ribosyltransferase activity / decidualization / site of DNA damage / Transferases; Glycosyltransferases; Pentosyltransferases / POLB-Dependent Long Patch Base Excision Repair / NAD+ poly-ADP-ribosyltransferase activity / nucleosome binding / extrinsic apoptotic signaling pathway / nucleotidyltransferase activity / base-excision repair / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / double-strand break repair / damaged DNA binding / DNA repair / DNA damage response / chromatin binding / nucleolus / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. ...: / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile.
Similarity search - Domain/homology
DNA / DNA (> 10) / Poly [ADP-ribose] polymerase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsObaji, E. / Haikarainen, T. / Lehtio, L.
Funding support Finland, 3items
OrganizationGrant numberCountry
Academy of Finland Finland
Jane and Aatos Erkko Foundation Finland
Biocenter Oulu, University of Oulu Finland
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural basis for DNA break recognition by ARTD2/PARP2.
Authors: Obaji, E. / Haikarainen, T. / Lehtio, L.
History
DepositionDec 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 2
B: Poly [ADP-ribose] polymerase 2
C: Poly [ADP-ribose] polymerase 2
D: Poly [ADP-ribose] polymerase 2
E: DNA (5'-D(P*CP*GP*GP*TP*CP*GP*CP*CP*TP*AP*TP*AP*GP*GP*C)-3')
F: DNA (5'-D(P*CP*GP*GP*TP*CP*GP*CP*CP*TP*AP*TP*AP*GP*GP*C)-3')
G: DNA (5'-D(P*CP*GP*GP*TP*CP*GP*CP*CP*TP*AP*TP*AP*GP*GP*C)-3')
H: DNA (5'-D(P*CP*GP*GP*TP*CP*GP*CP*CP*TP*AP*TP*AP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)79,4458
Polymers79,4458
Non-polymers00
Water00
1
A: Poly [ADP-ribose] polymerase 2
E: DNA (5'-D(P*CP*GP*GP*TP*CP*GP*CP*CP*TP*AP*TP*AP*GP*GP*C)-3')
F: DNA (5'-D(P*CP*GP*GP*TP*CP*GP*CP*CP*TP*AP*TP*AP*GP*GP*C)-3')

C: Poly [ADP-ribose] polymerase 2


Theoretical massNumber of molelcules
Total (without water)39,7224
Polymers39,7224
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
2
B: Poly [ADP-ribose] polymerase 2
D: Poly [ADP-ribose] polymerase 2
G: DNA (5'-D(P*CP*GP*GP*TP*CP*GP*CP*CP*TP*AP*TP*AP*GP*GP*C)-3')
H: DNA (5'-D(P*CP*GP*GP*TP*CP*GP*CP*CP*TP*AP*TP*AP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)39,7224
Polymers39,7224
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.150, 87.150, 185.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17E
27F
18E
28G
19E
29H
110F
210G
111F
211H
112G
212H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASPASPAA92 - 2075 - 120
21ALAALAASPASPBB92 - 2075 - 120
12ALAALAGLNGLNAA92 - 2055 - 118
22ALAALAGLNGLNCC92 - 2055 - 118
13ALAALALEULEUAA92 - 2045 - 117
23ALAALALEULEUDD92 - 2045 - 117
14ALAALAGLNGLNBB92 - 2055 - 118
24ALAALAGLNGLNCC92 - 2055 - 118
15ALAALALEULEUBB92 - 2045 - 117
25ALAALALEULEUDD92 - 2045 - 117
16ALAALALEULEUCC92 - 2045 - 117
26ALAALALEULEUDD92 - 2045 - 117
17DCDCDCDCEE1 - 151 - 15
27DCDCDCDCFF1 - 151 - 15
18DCDCDCDCEE1 - 151 - 15
28DCDCDCDCGG1 - 151 - 15
19DCDCDCDCEE1 - 151 - 15
29DCDCDCDCHH1 - 151 - 15
110DCDCDCDCFF1 - 151 - 15
210DCDCDCDCGG1 - 151 - 15
111DCDCDCDCFF1 - 151 - 15
211DCDCDCDCHH1 - 151 - 15
112DCDCDCDCGG1 - 151 - 15
212DCDCDCDCHH1 - 151 - 15

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
Poly [ADP-ribose] polymerase 2 / hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / NAD(+) ADP-ribosyltransferase 2 ...hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / NAD(+) ADP-ribosyltransferase 2 / ADPRT-2 / Poly[ADP-ribose] synthase 2 / pADPRT-2


Mass: 15275.181 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP2, ADPRT2, ADPRTL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UGN5, NAD+ ADP-ribosyltransferase
#2: DNA chain
DNA (5'-D(P*CP*GP*GP*TP*CP*GP*CP*CP*TP*AP*TP*AP*GP*GP*C)-3')


Mass: 4585.972 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: 3.46 Å3/Da / Density % sol: 64.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Na-formate 20 % PEG 3350 20 % glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.98→20 Å / Num. obs: 23275 / % possible obs: 99.8 % / Redundancy: 6.38 % / CC1/2: 0.88 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.075 / Net I/av σ(I): 1.35 / Net I/σ(I): 15.29
Reflection shellResolution: 2.98→3 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 6F1K

6f1k


Resolution: 2.98→19.86 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 25.197 / SU ML: 0.404 / Cross valid method: THROUGHOUT / ESU R: 1.13 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2753 1155 5 %RANDOM
Rwork0.22822 ---
obs0.23056 21936 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 121.612 Å2
Baniso -1Baniso -2Baniso -3
1-3.9 Å20 Å20 Å2
2--7.42 Å2-0 Å2
3----11.32 Å2
Refinement stepCycle: 1 / Resolution: 2.98→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3780 1232 0 0 5012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0175236
X-RAY DIFFRACTIONr_bond_other_d0.0020.024155
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.7177308
X-RAY DIFFRACTIONr_angle_other_deg1.17839731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8265457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53125.619210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.86815723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4171516
X-RAY DIFFRACTIONr_chiral_restr0.1150.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025019
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021089
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.4112.6411840
X-RAY DIFFRACTIONr_mcbond_other9.40112.6411839
X-RAY DIFFRACTIONr_mcangle_it13.98518.9472293
X-RAY DIFFRACTIONr_mcangle_other13.98218.9492294
X-RAY DIFFRACTIONr_scbond_it9.75512.1943396
X-RAY DIFFRACTIONr_scbond_other9.75512.1953395
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.35118.1165015
X-RAY DIFFRACTIONr_long_range_B_refined16.9656011
X-RAY DIFFRACTIONr_long_range_B_other16.9646012
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A73780.09
12B73780.09
21A71900.1
22C71900.1
31A71480.09
32D71480.09
41B72000.11
42C72000.11
51B71080.11
52D71080.11
61C70480.11
62D70480.11
71E23100.16
72F23100.16
81E22940.16
82G22940.16
91E22820.17
92H22820.17
101F24580.13
102G24580.13
111F25540.12
112H25540.12
121G24020.16
122H24020.16
LS refinement shellResolution: 2.98→3.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.48 82 -
Rwork0.483 1553 -
obs--99.7 %

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