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- PDB-9qyh: PARP9 Macro Domain 2 in complex with NAD+ -

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Basic information

Entry
Database: PDB / ID: 9qyh
TitlePARP9 Macro Domain 2 in complex with NAD+
ComponentsProtein mono-ADP-ribosyltransferase PARP9
KeywordsTRANSFERASE / PARP9 / MACRO DOMAIN / NAD+
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Protein mono-ADP-ribosyltransferase PARP9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 Regional Development Fund5002550-INSPIREDEuropean Union
European Union (EU)101087215-ESPERANCEEuropean Union
European Union (EU)101159708-MILESTONEEuropean Union
European Union (EU)871037-iNEXT DiscoveryEuropean 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

Downloads & links

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Assembly

Deposited unit
A: Protein mono-ADP-ribosyltransferase PARP9
B: Protein mono-ADP-ribosyltransferase PARP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7934
Polymers44,4662
Non-polymers1,3272
Water23413
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A: Protein mono-ADP-ribosyltransferase PARP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8962
Polymers22,2331
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein mono-ADP-ribosyltransferase PARP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8962
Polymers22,2331
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.428, 73.827, 58.465
Angle α, β, γ (deg.)90.00, 116.90, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 MES, 0.2M Ammonium chloride, 20% w/v PEG 6000

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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: Sep 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.5→73.83 Å / Num. obs: 13136 / % possible obs: 92.8 % / Redundancy: 3.1 % / CC1/2: 0.996 / Net I/σ(I): 7.9
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1491 / CC1/2: 0.714

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→52.19 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 35.336 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24602 1356 10.3 %RANDOM
Rwork0.19727 ---
obs0.20227 11763 92.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.358 Å2
Baniso -1Baniso -2Baniso -3
1-2.9 Å2-0 Å20.96 Å2
2---3.01 Å2-0 Å2
3----0.57 Å2
Refinement stepCycle: 1 / Resolution: 2.5→52.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 88 13 2964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123016
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162919
X-RAY DIFFRACTIONr_angle_refined_deg1.691.8224091
X-RAY DIFFRACTIONr_angle_other_deg0.5111.7586741
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6285356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.57356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4510549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023314
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02640
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_it3.3343.9371436
X-RAY DIFFRACTIONr_mcbond_other3.3333.9381437
X-RAY DIFFRACTIONr_mcangle_it5.3577.0631788
X-RAY DIFFRACTIONr_mcangle_other5.3577.0641789
X-RAY DIFFRACTIONr_scbond_it4.0094.5651580
X-RAY DIFFRACTIONr_scbond_other4.0084.5691581
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3518.262304
X-RAY DIFFRACTIONr_long_range_B_refined9.82440.213284
X-RAY DIFFRACTIONr_long_range_B_other9.82240.223285
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 113 -
Rwork0.377 869 -
obs--91.01 %
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)
16.1215-1.9468-1.06986.33951.2724.90110.08570.2841-0.5621-0.038-0.02120.20270.328-0.0942-0.06450.296-0.02660.00690.0192-0.04440.226818.0565-0.71215.3644
24.56590.1540.32385.74721.92075.3862-0.0791-0.11110.5482-0.04350.00970.2144-0.4055-0.32040.06950.27850.06280.05070.0329-0.03020.289511.997725.27715.3849
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A310 - 490
2X-RAY DIFFRACTION2B310 - 496

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