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- PDB-7s6h: Human PARP1 deltaV687-E688 bound to NAD+ analog EB-47 and to a DN... -

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Basic information

Entry
Database: PDB / ID: 7s6h
TitleHuman PARP1 deltaV687-E688 bound to NAD+ analog EB-47 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
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


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 / R-SMAD binding / nuclear replication fork / 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. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-UHB / DNA / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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

Downloads & links

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Assembly

Deposited unit
M: DNA (5'-D(*CP*GP*AP*CP*G)-3')
N: DNA (5'-D(*CP*GP*TP*CP*G)-3')
E: DNA (5'-D(*CP*GP*AP*CP*G)-3')
B: Poly [ADP-ribose] polymerase 1
F: 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)
D: Poly [ADP-ribose] polymerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,80816
Polymers182,3488
Non-polymers1,4618
Water18010
1
M: DNA (5'-D(*CP*GP*AP*CP*G)-3')
N: DNA (5'-D(*CP*GP*TP*CP*G)-3')
B: Poly [ADP-ribose] polymerase 1
A: Fusion of human PARP1 zinc fingers 1 and 3 (Zn1, Zn3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9048
Polymers91,1744
Non-polymers7304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*CP*GP*AP*CP*G)-3')
F: DNA (5'-D(*CP*GP*TP*CP*G)-3')
C: Fusion of human PARP1 zinc fingers 1 and 3 (Zn1, Zn3)
D: Poly [ADP-ribose] polymerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9048
Polymers91,1744
Non-polymers7304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.467, 110.651, 116.475
Angle α, β, γ (deg.)90.000, 115.060, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 9 or resid 11...
21(chain C and (resid 7 through 9 or resid 11...
12(chain B and (resid 531 through 646 or resid 662...
22(chain D and (resid 531 through 646 or resid 662...
13chain E
23chain M
14chain F
24chain N

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 7 through 9 or resid 11...A7 - 9
121(chain A and (resid 7 through 9 or resid 11...A11 - 90
131(chain A and (resid 7 through 9 or resid 11...A224
141(chain A and (resid 7 through 9 or resid 11...A226 - 229
151(chain A and (resid 7 through 9 or resid 11...A231 - 304
161(chain A and (resid 7 through 9 or resid 11...A306 - 500
211(chain C and (resid 7 through 9 or resid 11...C7 - 9
221(chain C and (resid 7 through 9 or resid 11...C11 - 224
231(chain C and (resid 7 through 9 or resid 11...C226 - 229
241(chain C and (resid 7 through 9 or resid 11...C231 - 304
251(chain C and (resid 7 through 9 or resid 11...C306 - 500
112(chain B and (resid 531 through 646 or resid 662...B531 - 646
122(chain B and (resid 531 through 646 or resid 662...B662 - 663
132(chain B and (resid 531 through 646 or resid 662...B665 - 778
142(chain B and (resid 531 through 646 or resid 662...B780
152(chain B and (resid 531 through 646 or resid 662...B788 - 808
162(chain B and (resid 531 through 646 or resid 662...B810 - 1102
172(chain B and (resid 531 through 646 or resid 662...B1103
212(chain D and (resid 531 through 646 or resid 662...D531 - 646
222(chain D and (resid 531 through 646 or resid 662...D662 - 663
232(chain D and (resid 531 through 646 or resid 662...D665 - 778
242(chain D and (resid 531 through 646 or resid 662...D780
252(chain D and (resid 531 through 646 or resid 662...D788 - 808
262(chain D and (resid 531 through 646 or resid 662...D810 - 1102
272(chain D and (resid 531 through 646 or resid 662...D1103
113chain EE1 - 5
213chain MM1 - 5
114chain FF22 - 26
214chain NN22 - 26

NCS ensembles :
ID
1
2
3
4

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Components

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DNA chain , 2 types, 4 molecules MENF

#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 BDAC

#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 , 4 types, 18 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-UHB / 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide


Mass: 537.528 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H27N9O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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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: 3.56 Å3/Da / Density % sol: 65.44 %
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: ALS / Beamline: 8.3.1 / Wavelength: 1.12 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 3.1→49 Å / Num. obs: 46570 / % possible obs: 99.7 % / Redundancy: 4.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.057 / Rrim(I) all: 0.126 / Net I/σ(I): 6.1 / Num. measured all: 212612 / Scaling rejects: 1
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
3.1-3.214.51.4722041745410.3740.7691.6680.699.9
12.01-494.20.05834968350.9970.0290.06514.998.3

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Processing

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

4dqy


Resolution: 3.1→48.52 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 2150 4.62 %
Rwork0.2105 44372 -
obs0.2123 46522 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 307.34 Å2 / Biso mean: 141.2093 Å2 / Biso min: 74.35 Å2
Refinement stepCycle: final / Resolution: 3.1→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10960 398 152 10 11520
Biso mean--120.09 94.37 -
Num. residues----1404
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1696X-RAY DIFFRACTIONPOSITIONAL0.006
12C1696X-RAY DIFFRACTIONPOSITIONAL0.006
21B3725X-RAY DIFFRACTIONPOSITIONAL0.081
22D3725X-RAY DIFFRACTIONPOSITIONAL0.081
31E100X-RAY DIFFRACTIONPOSITIONAL0.007
32M100X-RAY DIFFRACTIONPOSITIONAL0.007
41F99X-RAY DIFFRACTIONPOSITIONAL0.006
42N99X-RAY DIFFRACTIONPOSITIONAL0.006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.170.4111510.385729293080100
3.17-3.250.41561250.363929653090100
3.25-3.340.36511560.316229333089100
3.34-3.440.31951430.296929333076100
3.44-3.550.34191610.280829153076100
3.55-3.680.34211360.282329823118100
3.68-3.820.30951420.273129713113100
3.82-40.28351250.237329483073100
4-4.210.24561880.210629073095100
4.21-4.470.26171460.19242970311699
4.47-4.810.21521660.182729193085100
4.82-5.30.21561030.17573002310599
5.3-6.060.23251730.192629243097100
6.06-7.640.24241400.201829953135100
7.64-48.520.1895950.17743079317499
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)
10.04480.01630.00660.00580.0012-0.00080.1637-0.13560.317-0.5089-0.17960.94710.06150.2488-0.00061.1579-0.0146-0.16061.11910.17791.6394-2.601335.381166.705
20.02160.02320.01520.03180.03570.04650.079-0.18780.1294-0.5986-0.65950.7225-0.09860.90470.00011.44620.1232-0.21871.10350.22771.7204-5.642230.711760.9642
30.0489-0.00180.0499-0.0014-0.00030.0460.30750.08850.1278-0.3314-0.00891.42490.34280.1785-0.00041.2491-0.1193-0.23781.0695-0.01071.265-4.34411.066771.1625
43.1847-0.1529-1.55441.1695-0.10780.5228-0.08580.00930.11540.10260.1782-0.14940.13070.0432-01.24320.0044-0.08661.1909-0.03960.983142.052834.076356.8153
50.00120-0.00080.0398-0.0220.00950.001-0.07630.4033-0.1125-0.54221.0824-0.07210.6167-0.00031.3538-0.192-0.1691.10230.02161.7166-10.77365.637172.49
60.97230.13930.74070.9489-0.55350.86110.18650.53510.0767-0.7662-0.11950.25960.0814-0.21020.00011.56750.1561-0.37471.38810.03141.3379-8.655221.354445.6327
71.27220.1338-0.08561.1807-0.4921.56730.0437-0.0144-0.05040.283-0.14060.918-0.0425-0.66-0.00011.0699-0.01590.03281.4336-0.09291.8491-24.578614.778179.9296
80.25520.25571.41821.19120.02923.7260.0184-0.03930.00090.12340.0813-0.11520.32070.039200.97130.02590.15321.176-0.01661.172716.86872.6576111.543
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'M' and resid 1 through 5)M1 - 5
2X-RAY DIFFRACTION2(chain 'N' and resid 22 through 26)N22 - 26
3X-RAY DIFFRACTION3(chain 'E' and resid 1 through 5)E1 - 5
4X-RAY DIFFRACTION4(chain 'B' and resid 531 through 1102)B531 - 1102
5X-RAY DIFFRACTION5(chain 'F' and resid 22 through 26)F22 - 26
6X-RAY DIFFRACTION6(chain 'A' and resid 6 through 359)A6 - 359
7X-RAY DIFFRACTION7(chain 'C' and resid 6 through 359)C6 - 359
8X-RAY DIFFRACTION8(chain 'D' and resid 531 through 1102)D531 - 1102

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