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- PDB-8hlr: Human ADP-ribosyltransferase 1 (PARP1) catalytic domain bound to ... -

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Basic information

Entry
Database: PDB / ID: 8hlr
TitleHuman ADP-ribosyltransferase 1 (PARP1) catalytic domain bound to Fluzoparib (SHR3162)
ComponentsPoly [ADP-ribose] polymerase 1, processed C-terminus
KeywordsTRANSFERASE / DNA ADP-ribosyltransferase 1 / PARP1 / Fluzoparib / SHR3162
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 / positive regulation of myofibroblast differentiation / regulation of base-excision repair / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / positive regulation of single strand break repair / 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 / positive regulation of myofibroblast differentiation / regulation of base-excision repair / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / positive regulation of single strand break repair / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis / carbohydrate biosynthetic process / NAD+-protein-serine ADP-ribosyltransferase activity / regulation of catalytic activity / negative regulation of adipose tissue development / NAD DNA ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / mitochondrial DNA metabolic process / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / replication fork reversal / signal transduction involved in regulation of gene expression / positive regulation of necroptotic process / ATP generation from poly-ADP-D-ribose / transcription regulator activator activity / HDR through MMEJ (alt-NHEJ) / positive regulation of DNA-templated transcription, elongation / positive regulation of intracellular estrogen receptor signaling pathway / NAD+ ADP-ribosyltransferase / cellular response to zinc ion / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / mitochondrial DNA repair / response to aldosterone / protein poly-ADP-ribosylation / negative regulation of cGAS/STING signaling pathway / positive regulation of mitochondrial depolarization / positive regulation of cardiac muscle hypertrophy / nuclear replication fork / negative regulation of transcription elongation by RNA polymerase II / NAD+-protein ADP-ribosyltransferase activity / site of DNA damage / R-SMAD binding / positive regulation of SMAD protein signal transduction / protein autoprocessing / macrophage differentiation / decidualization / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / POLB-Dependent Long Patch Base Excision Repair / nucleosome binding / positive regulation of double-strand break repair via homologous recombination / SUMOylation of DNA damage response and repair proteins / protein localization to chromatin / negative regulation of innate immune response / telomere maintenance / nucleotidyltransferase activity / transforming growth factor beta receptor signaling pathway / cellular response to nerve growth factor stimulus / protein-DNA complex / mitochondrion organization / nuclear estrogen receptor binding / 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 / histone deacetylase binding / positive regulation of protein localization to nucleus / Formation of Incision Complex in GG-NER / cellular response to insulin stimulus / cellular response to amyloid-beta / cellular response to UV / NAD binding / double-strand break repair / nuclear envelope / regulation of protein localization / 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 / innate immune response / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / chromatin binding / chromatin / nucleolus / protein kinase binding / apoptotic process / negative regulation of transcription by RNA polymerase II / enzyme binding / 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
: / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsWang, X.Y. / Zhou, J. / Xu, B.L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82003657 China
National Natural Science Foundation of China (NSFC)81673300 China
National Natural Science Foundation of China (NSFC)82173693 China
CitationJournal: To Be Published
Title: Human ADP-ribosyltransferase 1 (PARP1) catalytic domain bound to Fluzoparib (SHR3162)
Authors: Wang, X.Y. / Zhou, J. / Xu, B.L.
History
DepositionNov 30, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 1, processed C-terminus
B: Poly [ADP-ribose] polymerase 1, processed C-terminus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,20816
Polymers79,1112
Non-polymers2,09814
Water57632
1
A: Poly [ADP-ribose] polymerase 1, processed C-terminus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6048
Polymers39,5551
Non-polymers1,0497
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-21 kcal/mol
Surface area16790 Å2
MethodPISA
2
B: Poly [ADP-ribose] polymerase 1, processed C-terminus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6048
Polymers39,5551
Non-polymers1,0497
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-21 kcal/mol
Surface area16760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.814, 92.746, 164.026
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Poly [ADP-ribose] polymerase 1, processed C-terminus / Poly [ADP-ribose] polymerase 1 / 89-kDa form


Mass: 39555.270 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
#2: Chemical ChemComp-25I / Fluzoparib / SHR3162


Mass: 472.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H16F4N6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 2.5 M ammonium sulfate, 100 mM Tris-HCl, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.85→46.79 Å / Num. obs: 17378 / % possible obs: 95.47 % / Redundancy: 7 % / Biso Wilson estimate: 47.57 Å2 / CC1/2: 0.997 / Net I/σ(I): 15.01
Reflection shellResolution: 2.85→2.952 Å / Num. unique obs: 1669 / CC1/2: 0.782

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Processing

Software
NameVersionClassification
autoPROCdata processing
Aimlessdata scaling
MOLREPphasing
REFMACv8refinement
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→46.79 Å / SU ML: 0.2552 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.599
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2881 827 4.78 %
Rwork0.2372 16466 -
obs0.2399 17293 95.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.4 Å2
Refinement stepCycle: LAST / Resolution: 2.85→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5504 0 128 32 5664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00275732
X-RAY DIFFRACTIONf_angle_d0.55787756
X-RAY DIFFRACTIONf_chiral_restr0.0397850
X-RAY DIFFRACTIONf_plane_restr0.004980
X-RAY DIFFRACTIONf_dihedral_angle_d18.95492158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.030.31361500.29822710X-RAY DIFFRACTION96.98
3.03-3.260.34521460.28172815X-RAY DIFFRACTION100
3.26-3.590.32191460.25892830X-RAY DIFFRACTION100
3.59-4.110.2368980.22822186X-RAY DIFFRACTION76.23
4.11-5.180.26341420.20342890X-RAY DIFFRACTION99.87
5.18-46.790.2871450.22453035X-RAY DIFFRACTION99.62

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