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- PDB-7aeo: Human ARTD2 in complex with DNA oligonucleotides -

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Basic information

Entry
Database: PDB / ID: 7aeo
TitleHuman ARTD2 in complex with DNA oligonucleotides
Components
  • (DNA) x 2
  • Poly [ADP-ribose] polymerase 2
KeywordsDNA BINDING PROTEIN / ARTD2 / PARP2 / DNA-damage / DNA-repair / ADP-ribosylation / DNA-binding protein
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 / Poly(ADP-ribose) Polymerase; domain 1 / : / 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 / Poly(ADP-ribose) Polymerase; domain 1 / : / 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. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Poly [ADP-ribose] polymerase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsObaji, E. / Maksimainen, M.M. / Galera-Prat, A. / Lehtio, L.
Funding support Finland, 4items
OrganizationGrant numberCountry
Jane and Aatos Erkko Foundation Finland
Academy of Finland287063 Finland
Academy of Finland294085 Finland
Academy of Finland319299 Finland
Citation
Journal: Nat Commun / Year: 2021
Title: Activation of PARP2/ARTD2 by DNA damage induces conformational changes relieving enzyme autoinhibition.
Authors: Obaji, E. / Maksimainen, M.M. / Galera-Prat, A. / Lehtio, L.
#1: Journal: Biorxiv / Year: 2020
Title: Activation of ARTD2/PARP2 by DNA damage induces conformational changes relieving enzyme autoinhibition
Authors: Obaji, E. / Maksimainen, M.M. / Galera-Prat, A. / Lehtio, L.
History
DepositionSep 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_entity_src_syn
Item: _entity.pdbx_description / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2Jun 23, 2021Group: Database references / Category: citation / citation_author
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: DNA
C: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7135
Polymers66,5213
Non-polymers1922
Water00
1
A: Poly [ADP-ribose] polymerase 2
B: DNA
C: DNA
hetero molecules

A: Poly [ADP-ribose] polymerase 2
B: DNA
C: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,42710
Polymers133,0426
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_556y,x,-z+11
Unit cell
Length a, b, c (Å)166.830, 166.830, 143.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-602-

SO4

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Components

#1: Protein Poly [ADP-ribose] polymerase 2 / hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / DNA ADP-ribosyltransferase PARP2 ...hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / DNA ADP-ribosyltransferase PARP2 / NAD(+) ADP-ribosyltransferase 2 / ADPRT-2 / Poly[ADP-ribose] synthase 2 / pADPRT-2 / Protein poly-ADP-ribosyltransferase PARP2


Mass: 56721.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP2, ADPRT2, ADPRTL2 / Production host: Escherichia coli BL21(DE3)
References: UniProt: Q9UGN5, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#2: DNA chain DNA


Mass: 4897.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA


Mass: 4902.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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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: 3.6 Å3/Da / Density % sol: 67.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sample was crystallized in 0.1 M MES pH 6.5 and 1 M ammonium sulfate. Cryo solution was a mixture of 10% (v/v) glycerol, 10% (v/v) diethylene glycol, and 10% (v/v) 2-propanol with the crystallization conditions

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9687 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9687 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 24990 / % possible obs: 98.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 98.91 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.12 / Net I/σ(I): 9.25
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.43 / Mean I/σ(I) obs: 1.59 / Num. unique obs: 1835 / CC1/2: 0.44 / Rrim(I) all: 1.56 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: F6IK and 5DSY

5dsy


Resolution: 2.8→26.84 Å / SU ML: 0.5859 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.9057
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2707 1175 4.7 %
Rwork0.2267 23803 -
obs0.2287 24978 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 142.96 Å2
Refinement stepCycle: LAST / Resolution: 2.8→26.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3606 654 10 0 4270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00534425
X-RAY DIFFRACTIONf_angle_d0.73876118
X-RAY DIFFRACTIONf_chiral_restr0.0432663
X-RAY DIFFRACTIONf_plane_restr0.0039678
X-RAY DIFFRACTIONf_dihedral_angle_d21.11431682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.930.52391350.42012950X-RAY DIFFRACTION99.55
2.93-3.080.36931460.35792951X-RAY DIFFRACTION99.68
3.08-3.270.30351420.24742958X-RAY DIFFRACTION99.33
3.27-3.530.23381400.24752934X-RAY DIFFRACTION99.23
3.53-3.880.26911580.25852964X-RAY DIFFRACTION99.14
3.88-4.440.2521530.22582975X-RAY DIFFRACTION99.59
4.44-5.580.2421540.20943002X-RAY DIFFRACTION98.97
5.59-26.840.27831470.19753069X-RAY DIFFRACTION97.01
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)
15.2436558459-0.713310405169-3.840488802251.966725159582.076420068592.89890648892-0.2783655916440.607540946793-0.488179571624-0.690992068126-0.01210501062650.502079609273-0.348853947794-0.276258094270.2861332701190.9845771354970.153734313238-0.1733352508141.273836589590.07274629186660.930762628972-9.44264449495-27.659984671151.356120158
24.829828658931.16252798149-0.01654221946914.21863738614-2.199383304916.08209766088-0.4257034044840.391051046719-0.12954642524-0.163183518177-0.1349619256220.492606754585-0.476765601406-0.6006032888490.5448191436671.088718477150.1064325787820.1518774616120.806454331516-0.254824593290.7243798903931.8278004539-25.853171800931.3169269313
34.76203451251-0.6218114195351.655433992974.97958001706-4.906587536375.115865397250.16657852094-0.884475494687-0.7819870354081.99130261222-0.860794718818-0.57416410642-0.07117153788391.409427495370.6647466743962.017222532240.351930832493-0.3273445737131.102780563470.245604066511.05221967776-28.854237186419.377096795947.8960434074
46.21287039393-5.797239649695.04017844465.49815018447-4.754783276214.128133217741.757000536911.08721680250.0725833851177-0.832246343125-0.2852569337191.52093224688-0.724645493893-0.691982374349-0.8887995629341.900997109490.420294402414-0.1557927586961.350196413450.5921280407051.68327627621-22.0502252897-0.61542012384763.2597531452
52.99599728795-3.772041980571.844166857885.86943334095-3.40531211533.221764617210.183382350110.9297455608510.4929641952010.6406475807050.3277556232260.201809378252-2.077957354580.57590526335-0.3233033289571.753213242030.4570189989-0.2286559497341.355583837740.3441599863361.38288795612-21.3442056533-1.7279665799364.2256408223
64.68384816079-4.571211943131.713446139764.52014057737-0.8805312317726.031654366010.4047013544531.16891136491-0.05944282409120.207937947743-1.20098785155-0.6352413008790.1965836114430.8758674955830.6385189462521.588340465710.3648773481920.03456619789491.312765720530.4982606757391.46453786774-34.776461188514.116259394248.0681783768
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 91 through 365 )AA91 - 3651 - 238
22chain 'A' and (resid 366 through 583 )AA366 - 583239 - 456
33chain 'B' and (resid 1 through 5 )BB1 - 5
44chain 'B' and (resid 6 through 16 )BB6 - 16
55chain 'C' and (resid 1 through 10 )CC1 - 10
66chain 'C' and (resid 11 through 16 )CC11 - 16

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