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- PDB-6m3i: Crystal structure of HPF1/PARP1 complex -

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Basic information

Entry
Database: PDB / ID: 6m3i
TitleCrystal structure of HPF1/PARP1 complex
Components
  • Histone PARylation factor 1
  • Poly [ADP-ribose] polymerase 1
KeywordsNUCLEAR PROTEIN / complex / ADP-ribosylation / DNA damage response
Function / homology
Function and homology information


regulation of protein ADP-ribosylation / protein ADP-ribosyltransferase-substrate adaptor activity / 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 / negative regulation of ATP biosynthetic process / poly-ADP-D-ribose binding / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity ...regulation of protein ADP-ribosylation / protein ADP-ribosyltransferase-substrate adaptor activity / 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 / negative regulation of ATP biosynthetic process / poly-ADP-D-ribose binding / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / regulation of base-excision repair / positive regulation of single strand break repair / regulation of circadian sleep/wake cycle, non-REM sleep / mitochondrial DNA metabolic process / vRNA Synthesis / carbohydrate biosynthetic process / NAD+-protein-serine ADP-ribosyltransferase activity / negative regulation of adipose tissue development / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / 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 / response to aldosterone / HDR through MMEJ (alt-NHEJ) / positive regulation of DNA-templated transcription, elongation / NAD+ ADP-ribosyltransferase / signal transduction involved in regulation of gene expression / protein auto-ADP-ribosylation / negative regulation of telomere maintenance via telomere lengthening / mitochondrial DNA repair / NAD+-protein-aspartate ADP-ribosyltransferase activity / 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 / DNA repair-dependent chromatin remodeling / positive regulation of cardiac muscle hypertrophy / NAD+-protein mono-ADP-ribosyltransferase activity / cellular response to zinc ion / positive regulation of mitochondrial depolarization / nuclear replication fork / decidualization / protein autoprocessing / R-SMAD binding / macrophage differentiation / Transferases; Glycosyltransferases; Pentosyltransferases / negative regulation of transcription elongation by RNA polymerase II / positive regulation of SMAD protein signal transduction / POLB-Dependent Long Patch Base Excision Repair / NAD+ poly-ADP-ribosyltransferase activity / site of DNA damage / SUMOylation of DNA damage response and repair proteins / nucleosome binding / positive regulation of double-strand break repair via homologous recombination / protein localization to chromatin / nucleotidyltransferase activity / transforming growth factor beta receptor signaling pathway / negative regulation of innate immune response / telomere maintenance / nuclear estrogen receptor binding / response to gamma radiation / mitochondrion organization / protein modification process / Downregulation of SMAD2/3:SMAD4 transcriptional activity / enzyme activator activity / protein-DNA complex / cellular response to nerve growth factor stimulus / positive regulation of protein localization to nucleus / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / cellular response to insulin stimulus / cellular response to amyloid-beta / histone deacetylase binding / NAD binding / Formation of Incision Complex in GG-NER / cellular response to UV / nuclear envelope / double-strand break repair / regulation of protein localization / site of double-strand break / cellular response to oxidative stress / histone binding / transcription regulator complex / transcription by RNA polymerase II / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / positive regulation of canonical NF-kappaB signal transduction / nuclear body / innate immune response / DNA repair / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / ubiquitin protein ligase binding / chromatin binding / protein kinase binding
Similarity search - Function
Histone PARylation factor 1 / Histone PARylation factor 1 / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 ...Histone PARylation factor 1 / Histone PARylation factor 1 / 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
BENZAMIDE / Poly [ADP-ribose] polymerase 1 / Histone PARylation factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsSun, F.H. / Yun, C.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31270769 China
CitationJournal: Nat Commun / Year: 2021
Title: HPF1 remodels the active site of PARP1 to enable the serine ADP-ribosylation of histones.
Authors: Sun, F.H. / Zhao, P. / Zhang, N. / Kong, L.L. / Wong, C.C.L. / Yun, C.H.
History
DepositionMar 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Histone PARylation factor 1
B: Poly [ADP-ribose] polymerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6733
Polymers67,5522
Non-polymers1211
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-14 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.858, 84.179, 81.731
Angle α, β, γ (deg.)90.000, 107.490, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Histone PARylation factor 1


Mass: 39495.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPF1, C4orf27
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q9NWY4
#2: 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: 28057.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP1, ADPRT, PPOL
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P09874, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#3: Chemical ChemComp-UNU / BENZAMIDE


Mass: 121.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 300 K / Method: vapor diffusion
Details: 0.1 M Tris-pH 7.0, 0.2 M magnesium formate dehydrate, 20% w/v PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97849 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Feb 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 44217 / % possible obs: 98.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 27.82 Å2 / Rpim(I) all: 0.053 / Net I/σ(I): 14.1
Reflection shellResolution: 1.98→2.03 Å / Num. unique obs: 2414 / Rpim(I) all: 0.385

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M3G, 6BHV

6m3g

6bhv


Resolution: 1.98→27.39 Å / SU ML: 0.2247 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 21.1342
RfactorNum. reflection% reflection
Rfree0.2064 2300 5.2 %
Rwork0.175 --
obs0.1766 44217 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.03 Å2
Refinement stepCycle: LAST / Resolution: 1.98→27.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4367 0 9 323 4699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00774474
X-RAY DIFFRACTIONf_angle_d0.90486047
X-RAY DIFFRACTIONf_chiral_restr0.0601667
X-RAY DIFFRACTIONf_plane_restr0.0049777
X-RAY DIFFRACTIONf_dihedral_angle_d18.91731657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.020.29611190.24822414X-RAY DIFFRACTION89.57
2.02-2.070.27581490.22952625X-RAY DIFFRACTION98.26
2.07-2.120.26131520.21352587X-RAY DIFFRACTION98.35
2.12-2.170.26361420.20612670X-RAY DIFFRACTION97.57
2.17-2.240.23431040.1952565X-RAY DIFFRACTION97.13
2.24-2.310.21371720.18582626X-RAY DIFFRACTION99.47
2.31-2.390.2151650.1842660X-RAY DIFFRACTION99.26
2.39-2.490.22611340.18042657X-RAY DIFFRACTION98.62
2.49-2.60.2451280.18692630X-RAY DIFFRACTION98.68
2.6-2.740.241770.18982594X-RAY DIFFRACTION97.71
2.74-2.910.22541500.19312570X-RAY DIFFRACTION96.49
2.91-3.130.22471490.19372661X-RAY DIFFRACTION99.22
3.13-3.450.19191320.17892664X-RAY DIFFRACTION99.4
3.45-3.950.20521390.1532634X-RAY DIFFRACTION97.68
3.95-4.970.13051310.1372667X-RAY DIFFRACTION97.9
4.97-27.390.18611570.15942693X-RAY DIFFRACTION98.31

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