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- PDB-7s6m: Human PARP1 deltaV687-E688 bound to a DNA double strand break. -

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Basic information

Entry
Database: PDB / ID: 7s6m
TitleHuman PARP1 deltaV687-E688 bound 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
KeywordsDNA BINDING PROTEIN/DNA / PARP / ADP-ribose transferase / DNA break detection / zinc finger / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / regulation of base-excision repair / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / carbohydrate biosynthetic process / regulation of circadian sleep/wake cycle, non-REM sleep ...NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / regulation of base-excision repair / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / carbohydrate biosynthetic process / regulation of circadian sleep/wake cycle, non-REM sleep / positive regulation of single strand break repair / vRNA Synthesis / negative regulation of adipose tissue development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / mitochondrial DNA metabolic process / DNA ADP-ribosylation / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / signal transduction involved in regulation of gene expression / positive regulation of necroptotic process / regulation of catalytic activity / ATP generation from poly-ADP-D-ribose / replication fork reversal / transcription regulator activator activity / HDR through MMEJ (alt-NHEJ) / positive regulation of DNA-templated transcription, elongation / NAD+ ADP-ribosyltransferase / cellular response to zinc ion / negative regulation of telomere maintenance via telomere lengthening / positive regulation of intracellular estrogen receptor signaling pathway / protein auto-ADP-ribosylation / positive regulation of mitochondrial depolarization / response to aldosterone / mitochondrial DNA repair / negative regulation of cGAS/STING signaling pathway / protein poly-ADP-ribosylation / positive regulation of cardiac muscle hypertrophy / negative regulation of transcription elongation by RNA polymerase II / nuclear replication fork / site of DNA damage / NAD+-protein ADP-ribosyltransferase activity / R-SMAD binding / positive regulation of SMAD protein signal transduction / protein autoprocessing / macrophage differentiation / decidualization / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of double-strand break repair via homologous recombination / NAD+ ADP-ribosyltransferase activity / POLB-Dependent Long Patch Base Excision Repair / nucleosome binding / SUMOylation of DNA damage response and repair proteins / protein localization to chromatin / negative regulation of innate immune response / telomere maintenance / nucleotidyltransferase activity / mitochondrion organization / transforming growth factor beta receptor signaling pathway / cellular response to nerve growth factor stimulus / nuclear estrogen receptor binding / protein-DNA complex / response to gamma radiation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / DNA Damage Recognition in GG-NER / protein modification process / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / histone deacetylase binding / positive regulation of protein localization to nucleus / cellular response to insulin stimulus / cellular response to amyloid-beta / NAD binding / cellular response to UV / regulation of protein localization / double-strand break repair / nuclear envelope / site of double-strand break / cellular response to oxidative stress / positive regulation of canonical NF-kappaB signal transduction / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / damaged DNA binding / chromosome, telomeric region / nuclear body / DNA repair / innate immune response / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / ubiquitin protein ligase binding / chromatin binding / chromatin / nucleolus / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity
Similarity search - Function
: / PADR1, N-terminal helical domain / PADR1 domain profile. / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / PADR1 domain, zinc ribbon fold / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily ...: / PADR1, N-terminal helical domain / PADR1 domain profile. / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / PADR1 domain, zinc ribbon fold / 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 / WGR domain profile. / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsRouleau-Turcotte, E. / Pascal, J.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT173370 Canada
CitationJournal: Mol.Cell / Year: 2022
Title: Captured snapshots of PARP1 in the active state reveal the mechanics of PARP1 allostery.
Authors: Rouleau-Turcotte, E. / Krastev, D.B. / Pettitt, S.J. / Lord, C.J. / Pascal, J.M.
History
DepositionSep 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 31, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)
C: Fusion of human PARP1 zinc fingers 1 and 3 (Zn1, Zn3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,79515
Polymers182,3488
Non-polymers4487
Water1086
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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3677
Polymers91,1744
Non-polymers1933
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4298
Polymers91,1744
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.705, 112.074, 116.482
Angle α, β, γ (deg.)90.000, 114.830, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 400 or resid 500))
21(chain C and (resid 6 through 91 or resid 227 through 400 or resid 500))
12(chain B and (resid 531 through 646 or resid 663...
22(chain D and (resid 531 through 646 or resid 663...
13chain M
23chain P
14chain N
24chain O

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 6 through 400 or resid 500))A0
211(chain C and (resid 6 through 91 or resid 227 through 400 or resid 500))C6 - 91
221(chain C and (resid 6 through 91 or resid 227 through 400 or resid 500))C227 - 400
231(chain C and (resid 6 through 91 or resid 227 through 400 or resid 500))C500
112(chain B and (resid 531 through 646 or resid 663...B531 - 646
122(chain B and (resid 531 through 646 or resid 663...B663
132(chain B and (resid 531 through 646 or resid 663...B665 - 689
142(chain B and (resid 531 through 646 or resid 663...B691 - 1020
152(chain B and (resid 531 through 646 or resid 663...B1101
212(chain D and (resid 531 through 646 or resid 663...D531 - 646
222(chain D and (resid 531 through 646 or resid 663...D663
232(chain D and (resid 531 through 646 or resid 663...D665 - 689
242(chain D and (resid 531 through 646 or resid 663...D691 - 780
252(chain D and (resid 531 through 646 or resid 663...D787 - 1020
262(chain D and (resid 531 through 646 or resid 663...D1101
113chain MM22 - 26
213chain PP22 - 26
114chain NN1 - 5
214chain OO1 - 5

NCS ensembles :
ID
1
2
3
4

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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.) synthetic construct (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.) synthetic construct (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 / Mutation: deltaV687-E688
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) / 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 , 3 types, 13 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.56 Å3/Da / Density % sol: 65.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.28 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 3.2→39.15 Å / Num. obs: 42258 / % possible obs: 99.7 % / Redundancy: 4.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.04 / Rrim(I) all: 0.083 / Net I/σ(I): 12.6 / Num. measured all: 175073
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.2-3.324.31.7291879544030.3150.9471.9790.999.5
11.97-39.153.90.02631818260.9980.0140.02948.596.5

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DQY

4dqy


Resolution: 3.2→39.15 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 1990 4.71 %
Rwork0.2064 40221 -
obs0.2081 42211 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 321.98 Å2 / Biso mean: 142.9915 Å2 / Biso min: 63.76 Å2
Refinement stepCycle: final / Resolution: 3.2→39.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10925 398 31 6 11360
Biso mean--121.27 78.62 -
Num. residues----1399
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1723X-RAY DIFFRACTIONPOSITIONAL0.013
12C1723X-RAY DIFFRACTIONPOSITIONAL0.013
21B3696X-RAY DIFFRACTIONPOSITIONAL0.052
22D3696X-RAY DIFFRACTIONPOSITIONAL0.052
31M99X-RAY DIFFRACTIONPOSITIONAL0.004
32P99X-RAY DIFFRACTIONPOSITIONAL0.004
41N100X-RAY DIFFRACTIONPOSITIONAL0.006
42O100X-RAY DIFFRACTIONPOSITIONAL0.006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.280.42031560.38792805296199
3.28-3.370.40371290.34752862299199
3.37-3.470.33921400.314828582998100
3.47-3.580.32341260.28282881300799
3.58-3.710.30591330.264228532986100
3.71-3.860.33251540.25228693023100
3.86-4.030.30111680.229928463014100
4.03-4.240.23661350.191428893024100
4.24-4.510.22341190.17728883007100
4.51-4.860.20271300.16928913021100
4.86-5.340.23591490.168328823031100
5.34-6.110.26881420.198128933035100
6.12-7.690.23811290.20692905303499
7.69-39.150.18371800.18372899307999
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)
10.0694-0.01930.05940.0165-0.01090.0477-0.5421-0.5921.1796-0.95050.26470.78080.12260.2471-0.00281.2181-0.0246-0.04261.20980.0591.3026-2.936535.715366.7593
20.0242-0.0064-0.01720.02150.05680.14180.5635-0.29850.2125-0.88-0.7994-0.41250.48560.96830.00011.58340.0774-0.12350.93570.17681.5465-6.003930.964661.0813
30.05860.03550.06440.02060.03670.06341.0068-0.051-0.0962-0.29680.24281.15730.38570.9330.00171.07440.0045-0.11781.08080.05141.225-4.84011.166971.4259
41.8709-0.3371-0.99231.06720.17620.1146-0.0011-0.05010.17650.2170.1383-0.26620.0867-0.0489-01.3422-0.0819-0.06591.24030.01751.05541.451334.594656.9827
5-0.17240.26331.09160.5750.15942.75070.03230.05460.05850.1620.0599-0.19380.39060.0730.00011.10060.05180.14211.2390.06651.19916.29942.7529111.8017
60.012-0.01780.01560.0248-0.03290.04420.9567-0.6363-0.25040.2981-0.40690.81730.01930.3973-0.00091.249-0.0560.11710.88430.06561.5236-11.17755.830372.8166
71.15150.4021-0.72361.0044-0.72021.18620.1651-0.09920.11910.3548-0.14470.6258-0.352-0.3765-0.00020.97640.0210.06051.2001-0.07411.5292-24.487415.153580.0353
81.3825-0.24680.41251.1637-0.74271.28440.1080.29640.0333-0.7501-0.20580.04380.03210.1045-0.00021.40750.0922-0.26931.1455-0.00211.0994-8.947821.534745.8347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'O' and resid 1 through 5)O1 - 5
2X-RAY DIFFRACTION2(chain 'P' and resid 22 through 26)P22 - 26
3X-RAY DIFFRACTION3(chain 'N' and resid 1 through 5)N1 - 5
4X-RAY DIFFRACTION4(chain 'D' and resid 531 through 1020)D531 - 1020
5X-RAY DIFFRACTION5(chain 'B' and resid 531 through 1020)B531 - 1020
6X-RAY DIFFRACTION6(chain 'M' and resid 22 through 26)M22 - 26
7X-RAY DIFFRACTION7(chain 'A' and resid 6 through 359)A6 - 359
8X-RAY DIFFRACTION8(chain 'C' and resid 6 through 359)C6 - 359

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