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- PDB-9qyf: PARP9 Macro Domain 2 in complex with ADPr -

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Basic information

Entry
Database: PDB / ID: 9qyf
TitlePARP9 Macro Domain 2 in complex with ADPr
ComponentsProtein mono-ADP-ribosyltransferase PARP9
KeywordsTRANSFERASE / Complex / ADP-ribose / ADPribosylation / PARP9 / Macro domain
Function / homology
Function and homology information


regulation of response to type II interferon / NAD+-protein-C-terminal glycine ADP-ribosyltransferase activity / ADP-D-ribose binding / positive regulation of type II interferon-mediated signaling pathway / negative regulation of catalytic activity / : / Nicotinamide salvage / Maturation of nucleoprotein / positive regulation of chromatin binding / Maturation of nucleoprotein ...regulation of response to type II interferon / NAD+-protein-C-terminal glycine ADP-ribosyltransferase activity / ADP-D-ribose binding / positive regulation of type II interferon-mediated signaling pathway / negative regulation of catalytic activity / : / Nicotinamide salvage / Maturation of nucleoprotein / positive regulation of chromatin binding / Maturation of nucleoprotein / positive regulation of tyrosine phosphorylation of STAT protein / STAT family protein binding / post-transcriptional regulation of gene expression / enzyme inhibitor activity / ubiquitin-like protein ligase binding / site of DNA damage / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of defense response to virus by host / nucleotidyltransferase activity / DNA damage checkpoint signaling / positive regulation of protein localization to nucleus / transcription corepressor activity / cell migration / double-strand break repair / defense response to virus / histone binding / viral protein processing / innate immune response / negative regulation of gene expression / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
PARP14-like, eighth type I KH domain / : / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / Chem-AR6 / Protein mono-ADP-ribosyltransferase PARP9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsFourkiotis, K.N. / Chikunova, A. / Tsika, C.A. / Kravvariti, P.K. / Tsatsouli, A.S. / Perrakis, A. / Spyroulias, A.G.
Funding supportEuropean Union, 4items
OrganizationGrant numberCountry
European Union (EU)101087215-ESPERANCEEuropean Union
European Union (EU)871037-iNEXT-DiscoveryEuropean Union
European Regional Development Fund5002550-INSPIREDEuropean Union
European Union (EU)101159708-MILESTONEEuropean Union
CitationJournal: To Be Published
Title: Comparative analysis of hPARP9 macro domains
Authors: Fourkiotis, K.N. / Chikunova, A. / Tsika, C.A. / Kravvariti, P.K. / Tsatsouli, A.S. / Perrakis, A. / Spyroulias, A.G.
History
DepositionApr 17, 2025Deposition site: PDBE / Processing site: PDBE
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 PARP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3513
Polymers22,2331
Non-polymers1,1192
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-7 kcal/mol
Surface area9290 Å2
Unit cell
Length a, b, c (Å)52.143, 52.143, 132.158
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein mono-ADP-ribosyltransferase PARP9 / ADP-ribosyltransferase diphtheria toxin-like 9 / ARTD9 / B aggressive lymphoma protein / Poly [ADP- ...ADP-ribosyltransferase diphtheria toxin-like 9 / ARTD9 / B aggressive lymphoma protein / Poly [ADP-ribose] polymerase 9 / PARP-9


Mass: 22232.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP9, BAL, BAL1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8IXQ6, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.02 Å3/Da / Density % sol: 39.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Succinic acid, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.3→40.93 Å / Num. obs: 45496 / % possible obs: 99.4 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 17
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 2206 / CC1/2: 0.698

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→40.97 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.304 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17313 2255 5 %RANDOM
Rwork0.13325 ---
obs0.13517 43241 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.498 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20 Å2
2--1.69 Å20 Å2
3----3.38 Å2
Refinement stepCycle: 1 / Resolution: 1.3→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 72 211 1801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121697
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161615
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.8212316
X-RAY DIFFRACTIONr_angle_other_deg0.6051.7593738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6935204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.22552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00710308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021886
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02364
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_it4.7461.649798
X-RAY DIFFRACTIONr_mcbond_other4.7031.648798
X-RAY DIFFRACTIONr_mcangle_it6.372.9711008
X-RAY DIFFRACTIONr_mcangle_other6.3832.9731009
X-RAY DIFFRACTIONr_scbond_it6.9691.966899
X-RAY DIFFRACTIONr_scbond_other6.9651.966900
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.5473.4741309
X-RAY DIFFRACTIONr_long_range_B_refined13.87124.11933
X-RAY DIFFRACTIONr_long_range_B_other12.519.261867
X-RAY DIFFRACTIONr_rigid_bond_restr3.90233312
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 175 -
Rwork0.233 3122 -
obs--99.13 %

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