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- PDB-9dfo: PARP4 BRCT domain K31Q mutant -

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Basic information

Entry
Database: PDB / ID: 9dfo
TitlePARP4 BRCT domain K31Q mutant
ComponentsProtein mono-ADP-ribosyltransferase PARP4
KeywordsTRANSFERASE / PARP family / ADP-ribosyltransferase / marylation / vault
Function / homology
Function and homology information


Nicotinamide salvage / Maturation of nucleoprotein / NAD+-protein-glutamate ADP-ribosyltransferase activity / Maturation of nucleoprotein / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / spindle microtubule ...Nicotinamide salvage / Maturation of nucleoprotein / NAD+-protein-glutamate ADP-ribosyltransferase activity / Maturation of nucleoprotein / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / spindle microtubule / protein modification process / inflammatory response / response to xenobiotic stimulus / ribonucleoprotein complex / DNA repair / DNA damage response / enzyme binding / DNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Protein mono-ADP-ribosyltransferase PARP4 / VIT domain / Vault protein inter-alpha-trypsin domain / VIT domain profile. / Vault protein Inter-alpha-Trypsin domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / von Willebrand factor type A domain / BRCA1 C Terminus (BRCT) domain ...Protein mono-ADP-ribosyltransferase PARP4 / VIT domain / Vault protein inter-alpha-trypsin domain / VIT domain profile. / Vault protein Inter-alpha-Trypsin domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / von Willebrand factor type A domain / 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 / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / BRCT domain profile. / BRCT domain / BRCT domain superfamily / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Protein mono-ADP-ribosyltransferase PARP4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFrigon, L. / Pascal, J.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT153295 Canada
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Crystal structure and mutagenesis of a nucleic acid-binding BRCT domain in human PARP4
Authors: Frigon, L. / Pascal, J.M.
History
DepositionAug 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein mono-ADP-ribosyltransferase PARP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8072
Polymers11,7111
Non-polymers961
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.769, 114.769, 114.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

21A-362-

HOH

31A-397-

HOH

41A-409-

HOH

51A-410-

HOH

61A-417-

HOH

71A-420-

HOH

81A-431-

HOH

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Components

#1: Protein Protein mono-ADP-ribosyltransferase PARP4 / 193 kDa vault protein / ADP-ribosyltransferase diphtheria toxin-like 4 / ARTD4 / PARP- ...193 kDa vault protein / ADP-ribosyltransferase diphtheria toxin-like 4 / ARTD4 / PARP-related/IalphaI-related H5/proline-rich / PH5P / Poly [ADP-ribose] polymerase 4 / PARP-4 / Vault poly(ADP-ribose) polymerase / VPARP


Mass: 11710.606 Da / Num. of mol.: 1 / Mutation: K31Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP4, ADPRTL1, KIAA0177, PARPL / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UKK3, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 31% PEG3350, 0.2M ammonium sulfate and 0.1M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.2 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 9972 / % possible obs: 99.9 % / Redundancy: 8.6 % / CC1/2: 1 / Net I/σ(I): 36.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 8.1 % / Num. unique obs: 653 / CC1/2: 0.837 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.41 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 6.287 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20843 516 5.2 %RANDOM
Rwork0.17025 ---
obs0.17215 9453 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.53 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→19.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms775 0 5 133 913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.012826
X-RAY DIFFRACTIONr_bond_other_d0.0010.016799
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.8131122
X-RAY DIFFRACTIONr_angle_other_deg0.4341.7931850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1385101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.64952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.60410156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02959
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02191
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.352.424389
X-RAY DIFFRACTIONr_mcbond_other1.3492.424389
X-RAY DIFFRACTIONr_mcangle_it2.1044.335489
X-RAY DIFFRACTIONr_mcangle_other2.1034.348490
X-RAY DIFFRACTIONr_scbond_it2.0562.781437
X-RAY DIFFRACTIONr_scbond_other2.0232.726434
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2784.894626
X-RAY DIFFRACTIONr_long_range_B_refined8.2225.97995
X-RAY DIFFRACTIONr_long_range_B_other8.11224.88941
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 26 -
Rwork0.238 716 -
obs--99.73 %
Refinement TLS params.Method: refined / Origin x: 13.2937 Å / Origin y: 3.3899 Å / Origin z: 25.4318 Å
111213212223313233
T0.013 Å2-0.0062 Å2-0.0183 Å2-0.0492 Å20.028 Å2--0.0433 Å2
L6.2233 °20.0787 °2-1.8406 °2-1.9701 °2-0.2914 °2--4.4243 °2
S-0.1039 Å °-0.448 Å °-0.0652 Å °-0.0079 Å °-0.0148 Å °-0.0633 Å °0.0677 Å °0.0654 Å °0.1186 Å °

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