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- PDB-9qyg: PARP9 Macro Domain 2 Free form -

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Basic information

Entry
Database: PDB / ID: 9qyg
TitlePARP9 Macro Domain 2 Free form
ComponentsProtein mono-ADP-ribosyltransferase PARP9
KeywordsTRANSFERASE / PARP9 / MACRO DOMAIN / FREE
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
Protein mono-ADP-ribosyltransferase PARP9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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)45,3135
Polymers44,4662
Non-polymers8473
Water905
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-10 kcal/mol
Surface area16470 Å2
Unit cell
Length a, b, c (Å)47.478, 73.294, 58.066
Angle α, β, γ (deg.)90.00, 113.27, 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-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M MIB, 25% w/v PEG 1500

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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: 2.7→73.29 Å / Num. obs: 9568 / % possible obs: 94.3 % / Redundancy: 3.2 % / CC1/2: 0.998 / Net I/σ(I): 12.1
Reflection shellResolution: 2.7→2.83 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1312 / CC1/2: 0.959

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→43.65 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.9 / SU B: 32.747 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 885 9.3 %RANDOM
Rwork0.18331 ---
obs0.19058 8681 94.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.098 Å2
Baniso -1Baniso -2Baniso -3
1-4.42 Å20 Å22.93 Å2
2---5.54 Å2-0 Å2
3----1.02 Å2
Refinement stepCycle: 1 / Resolution: 2.7→43.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2879 0 57 5 2941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122991
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162963
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.8214018
X-RAY DIFFRACTIONr_angle_other_deg0.4841.7526859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0545358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.34552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59510553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023263
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02617
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_it3.8214.5561444
X-RAY DIFFRACTIONr_mcbond_other3.8194.5561445
X-RAY DIFFRACTIONr_mcangle_it5.9968.1761798
X-RAY DIFFRACTIONr_mcangle_other5.9968.1761799
X-RAY DIFFRACTIONr_scbond_it4.1844.9581547
X-RAY DIFFRACTIONr_scbond_other4.1824.9591548
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5038.9272221
X-RAY DIFFRACTIONr_long_range_B_refined9.42445.23190
X-RAY DIFFRACTIONr_long_range_B_other9.42345.23191
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 52 -
Rwork0.225 684 -
obs--96.08 %
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)
13.8934-0.6661-0.51843.99070.12772.71740.08040.1372-0.2688-0.222-0.08780.15550.1211-0.10750.00740.0417-0.01210.02380.0176-0.03340.082916.8043-0.31556.0816
22.35620.52310.81243.73960.37644.23050.0101-0.01920.23720.0019-0.1050.2811-0.207-0.2760.09490.06560.03360.06740.02770.01560.119610.856624.526616.946
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A310 - 502
2X-RAY DIFFRACTION2B309 - 501

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