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- PDB-8g0h: Human PARP1 deltaV687-E688 bound to UKTT5 (compound 10) and to a ... -

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Basic information

Entry
Database: PDB / ID: 8g0h
TitleHuman PARP1 deltaV687-E688 bound to UKTT5 (compound 10) and to a DNA double strand break.
Components
  • DNA (5'-D(*CP*GP*AP*CP*G)-3')
  • DNA (5'-D(*CP*GP*TP*CP*G)-3')
  • Fusion of human PARP1 zinc fingers 1 and 3 (Zn1, Zn3),Poly [ADP-ribose] polymerase 1
  • Poly [ADP-ribose] polymerase 1
KeywordsDNA binding protein/DNA / PARP / ADP-ribose transferase / DNA break detection / Zinc finger / DNA binding protein-DNA complex
Function / homology
Function and homology information


positive regulation of myofibroblast differentiation / regulation of base-excision repair / NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis ...positive regulation of myofibroblast differentiation / regulation of base-excision repair / NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis / positive regulation of single strand break repair / carbohydrate biosynthetic process / NAD+-protein-serine ADP-ribosyltransferase activity / regulation of catalytic activity / negative regulation of adipose tissue development / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / mitochondrial DNA metabolic process / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / replication fork reversal / ATP generation from poly-ADP-D-ribose / positive regulation of necroptotic process / transcription regulator activator activity / HDR through MMEJ (alt-NHEJ) / positive regulation of DNA-templated transcription, elongation / signal transduction involved in regulation of gene expression / NAD+ ADP-ribosyltransferase / cellular response to zinc ion / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / NAD+-protein-aspartate ADP-ribosyltransferase activity / mitochondrial DNA repair / protein poly-ADP-ribosylation / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of cGAS/STING signaling pathway / NAD+-protein-glutamate ADP-ribosyltransferase activity / response to aldosterone / positive regulation of mitochondrial depolarization / positive regulation of cardiac muscle hypertrophy / NAD+-protein mono-ADP-ribosyltransferase activity / nuclear replication fork / R-SMAD binding / negative regulation of transcription elongation by RNA polymerase II / protein autoprocessing / site of DNA damage / macrophage differentiation / NAD+ poly-ADP-ribosyltransferase activity / decidualization / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of SMAD protein signal transduction / POLB-Dependent Long Patch Base Excision Repair / positive regulation of double-strand break repair via homologous recombination / SUMOylation of DNA damage response and repair proteins / nucleosome binding / protein localization to chromatin / nucleotidyltransferase activity / telomere maintenance / transforming growth factor beta receptor signaling pathway / negative regulation of innate immune response / nuclear estrogen receptor binding / response to gamma radiation / mitochondrion organization / Downregulation of SMAD2/3:SMAD4 transcriptional activity / cellular response to nerve growth factor stimulus / DNA Damage Recognition in GG-NER / protein-DNA complex / protein modification process / positive regulation of protein localization to nucleus / Dual Incision in GG-NER / histone deacetylase binding / Formation of Incision Complex in GG-NER / cellular response to insulin stimulus / cellular response to amyloid-beta / NAD binding / cellular response to UV / nuclear envelope / double-strand break repair / regulation of protein localization / site of double-strand break / cellular response to oxidative stress / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / damaged DNA binding / positive regulation of canonical NF-kappaB signal transduction / chromosome, telomeric region / nuclear body / innate immune response / DNA repair / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / DNA damage response / chromatin binding / protein kinase binding / chromatin / nucleolus / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity
Similarity search - Function
Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily ...Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger, PARP-type / : / 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. / BRCA1 C Terminus (BRCT) domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily
Similarity search - Domain/homology
: / DNA / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsRouleau-Turcotte, E. / Pascal, J.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT173370 Canada
CitationJournal: Biochem.J. / Year: 2024
Title: Novel modifications of PARP inhibitor veliparib increase PARP1 binding to DNA breaks.
Authors: Velagapudi, U.K. / Rouleau-Turcotte, E. / Billur, R. / Shao, X. / Patil, M. / Black, B.E. / Pascal, J.M. / Talele, T.T.
History
DepositionJan 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
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 1.2Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: DNA (5'-D(*CP*GP*AP*CP*G)-3')
P: DNA (5'-D(*CP*GP*TP*CP*G)-3')
N: DNA (5'-D(*CP*GP*AP*CP*G)-3')
D: Poly [ADP-ribose] polymerase 1
B: Poly [ADP-ribose] polymerase 1
M: DNA (5'-D(*CP*GP*TP*CP*G)-3')
A: Fusion of human PARP1 zinc fingers 1 and 3 (Zn1, Zn3),Poly [ADP-ribose] polymerase 1
C: Fusion of human PARP1 zinc fingers 1 and 3 (Zn1, Zn3),Poly [ADP-ribose] polymerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,45814
Polymers182,3488
Non-polymers1,1116
Water00
1
O: DNA (5'-D(*CP*GP*AP*CP*G)-3')
P: DNA (5'-D(*CP*GP*TP*CP*G)-3')
D: Poly [ADP-ribose] polymerase 1
C: Fusion of human PARP1 zinc fingers 1 and 3 (Zn1, Zn3),Poly [ADP-ribose] polymerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7297
Polymers91,1744
Non-polymers5553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-17 kcal/mol
Surface area37000 Å2
MethodPISA
2
N: DNA (5'-D(*CP*GP*AP*CP*G)-3')
B: Poly [ADP-ribose] polymerase 1
M: DNA (5'-D(*CP*GP*TP*CP*G)-3')
A: Fusion of human PARP1 zinc fingers 1 and 3 (Zn1, Zn3),Poly [ADP-ribose] polymerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7297
Polymers91,1744
Non-polymers5553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-19 kcal/mol
Surface area36780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.066, 110.172, 117.086
Angle α, β, γ (deg.)90.00, 114.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 4 molecules ONPM

#1: DNA chain DNA (5'-D(*CP*GP*AP*CP*G)-3')


Mass: 1505.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#2: DNA chain DNA (5'-D(*CP*GP*TP*CP*G)-3')


Mass: 1496.011 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)

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Protein , 2 types, 4 molecules DBAC

#3: Protein Poly [ADP-ribose] polymerase 1 / PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 ...PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1 / Protein poly-ADP-ribosyltransferase PARP1


Mass: 56909.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP1, ADPRT, PPOL / Production host: Escherichia coli (E. coli)
References: UniProt: P09874, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#4: Protein Fusion of human PARP1 zinc fingers 1 and 3 (Zn1, Zn3),Poly [ADP-ribose] polymerase 1 / PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 ...PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1 / Protein poly-ADP-ribosyltransferase PARP1


Mass: 31262.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP1, ADPRT, PPOL / Production host: Escherichia coli (E. coli)
References: UniProt: P09874, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases

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Non-polymers , 2 types, 6 molecules

#5: Chemical ChemComp-YH0 / 2-(4-{[2-(1H-benzimidazol-2-yl)ethyl]carbamoyl}phenyl)-1H-benzimidazole-7-carboxamide


Mass: 424.455 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H20N6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY

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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: 3.47 Å3/Da / Density % sol: 64.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 12% PEG6000 and 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 3.8→110.17 Å / Num. obs: 24750 / % possible obs: 99.6 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.081 / Rrim(I) all: 0.182 / Χ2: 1.15 / Net I/σ(I): 6.1 / Num. measured all: 115824
Reflection shellResolution: 3.8→4.06 Å / % possible obs: 99.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 2.642 / Num. measured all: 21838 / Num. unique obs: 4460 / CC1/2: 0.226 / Rpim(I) all: 1.31 / Rrim(I) all: 2.961 / Χ2: 1.07 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.19.2_4159refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7S6M

7s6m


Resolution: 3.8→76.59 Å / SU ML: 0.68 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3056 1286 5.21 %
Rwork0.2404 --
obs0.2436 24664 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→76.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11021 398 68 0 11487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211778
X-RAY DIFFRACTIONf_angle_d0.50515976
X-RAY DIFFRACTIONf_dihedral_angle_d13.8494466
X-RAY DIFFRACTIONf_chiral_restr0.0391729
X-RAY DIFFRACTIONf_plane_restr0.0032038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.950.38911470.38272522X-RAY DIFFRACTION97
3.95-4.130.40391440.37132578X-RAY DIFFRACTION99
4.13-4.350.35591580.32162587X-RAY DIFFRACTION100
4.35-4.620.33481170.27872622X-RAY DIFFRACTION100
4.62-4.980.30011380.25842600X-RAY DIFFRACTION100
4.98-5.480.32221670.25342587X-RAY DIFFRACTION100
5.48-6.270.34971460.27762597X-RAY DIFFRACTION100
6.27-7.90.30891440.25562624X-RAY DIFFRACTION99
7.9-76.590.25251250.17492661X-RAY DIFFRACTION98
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)
10.0086-0.0161-0.01910.0808-0.05250.0107-0.7388-0.4230.3973-0.4702-0.68010.9144-0.0242-1.08470.00221.6097-0.225-0.3342.21160.08982.7393-3.146635.506568.0375
20.05790.023-0.06270.01070.00370.12120.33410.459-0.669-0.18950.14030.54850.62281.76820.00072.7305-0.14130.11621.6217-0.26333.3421-6.069630.922662.3177
30.040.04270.02470.06740.05390.04491.03350.6195-0.33730.6599-1.41741.2782-0.3531-0.64020.00082.51780.1278-0.14192.0683-0.1011.9318-4.58830.922972.1537
42.57940.2964-2.45181.0618-0.1992-0.1736-0.10950.11440.36530.2040.11640.04720.3035-0.2185-0.00012.0235-0.0238-0.14362.08680.14671.671340.99134.293157.592
5-0.46640.07121.4848-0.04931.0823.9289-0.06130.0126-0.1167-0.28280.2035-0.2959-0.0330.056702.002-0.06130.16992.01950.08621.817916.11222.4071112.4267
60.022-0.0017-0.00750.02790.01780.0148-1.2339-0.22071.3150.37230.48261.23310.07341.29590.00092.44370.26260.05662.076-0.35062.7563-10.83115.320773.5152
72.18041.08550.03731.4997-0.86221.8990.2197-0.26380.33660.9887-0.44791.27920.3652-0.4150.00011.7942-0.10470.31031.8546-0.21343.0049-24.404614.286481.0127
81.69350.5880.85980.5314-0.00571.87510.13950.79050.0454-1.1942-0.2676-0.05950.0522-0.08040.00022.33380.0907-0.42582.2035-0.23562.0153-8.645821.744546.7052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'O' and resid 1 through 5)
2X-RAY DIFFRACTION2(chain 'P' and resid 22 through 26)
3X-RAY DIFFRACTION3(chain 'N' and resid 1 through 5)
4X-RAY DIFFRACTION4(chain 'D' and resid 531 through 1020)
5X-RAY DIFFRACTION5(chain 'B' and resid 531 through 1020)
6X-RAY DIFFRACTION6(chain 'M' and resid 22 through 26)
7X-RAY DIFFRACTION7(chain 'A' and resid 6 through 359)
8X-RAY DIFFRACTION8(chain 'C' and resid 3 through 361)

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