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- PDB-6we2: Human PARP14 (ARTD8), catalytic fragment in complex with RBN012759 -

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Basic information

Entry
Database: PDB / ID: 6we2
TitleHuman PARP14 (ARTD8), catalytic fragment in complex with RBN012759
ComponentsIsoform 1 of Protein mono-ADP-ribosyltransferase PARP14
KeywordsTRANSFERASE/Inhibitor / PARP14 / ARTD8 / monoPARP / ADP ribosylation / inhibitor complex / TRANSFERASE-Inhibitor complex
Function / homology
Function and homology information


positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases ...positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / positive regulation of tyrosine phosphorylation of STAT protein / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / innate immune response / enzyme binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PARP-14, RNA recognition motif 2 / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Macro domain / Appr-1"-p processing enzyme ...PARP-14, RNA recognition motif 2 / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Chem-XBA / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsSwinger, K.K. / Schenkel, L.B. / Kuntz, K.W.
CitationJournal: Cell Chem Biol / Year: 2021
Title: A potent and selective PARP14 inhibitor decreases protumor macrophage gene expression and elicits inflammatory responses in tumor explants.
Authors: Schenkel, L.B. / Molina, J.R. / Swinger, K.K. / Abo, R. / Blackwell, D.J. / Lu, A.Z. / Cheung, A.E. / Church, W.D. / Kunii, K. / Kuplast-Barr, K.G. / Majer, C.R. / Minissale, E. / Mo, J.R. / ...Authors: Schenkel, L.B. / Molina, J.R. / Swinger, K.K. / Abo, R. / Blackwell, D.J. / Lu, A.Z. / Cheung, A.E. / Church, W.D. / Kunii, K. / Kuplast-Barr, K.G. / Majer, C.R. / Minissale, E. / Mo, J.R. / Niepel, M. / Reik, C. / Ren, Y. / Vasbinder, M.M. / Wigle, T.J. / Richon, V.M. / Keilhack, H. / Kuntz, K.W.
History
DepositionApr 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 1 of Protein mono-ADP-ribosyltransferase PARP14
B: Isoform 1 of Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1275
Polymers43,3082
Non-polymers8193
Water32418
1
A: Isoform 1 of Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0953
Polymers21,6541
Non-polymers4412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 1 of Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0322
Polymers21,6541
Non-polymers3781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.500, 84.050, 80.890
Angle α, β, γ (deg.)90.00, 116.02, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 1613 - 1801 / Label seq-ID: 1 - 189

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Isoform 1 of Protein mono-ADP-ribosyltransferase PARP14 / ADP-ribosyltransferase diphtheria toxin-like 8 / ARTD8 / B aggressive lymphoma protein 2 / Poly ...ADP-ribosyltransferase diphtheria toxin-like 8 / ARTD8 / B aggressive lymphoma protein 2 / Poly [ADP-ribose] polymerase 14 / PARP-14


Mass: 21654.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP14, BAL2, KIAA1268 / Production host: Escherichia coli (E. coli)
References: UniProt: Q460N5, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-XBA / 7-(cyclopropylmethoxy)-5-fluoro-2-{[(trans-4-hydroxycyclohexyl)sulfanyl]methyl}quinazolin-4(3H)-one


Mass: 378.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23FN2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate; 0.1 M tri-Sodium citrate pH 5.6; 25 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.66→42.06 Å / Num. obs: 13344 / % possible obs: 98.8 % / Redundancy: 4 % / Biso Wilson estimate: 43.163 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 7.6
Reflection shellResolution: 2.66→2.79 Å / Redundancy: 4 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 2 / Num. unique obs: 955 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3smj

3smj


Resolution: 2.66→42.06 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.867 / SU B: 21.815 / SU ML: 0.415 / Cross valid method: THROUGHOUT / ESU R: 1.279 / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29596 689 4.9 %RANDOM
Rwork0.24591 ---
obs0.24825 13344 96.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.163 Å2
Baniso -1Baniso -2Baniso -3
1-4.8 Å2-0 Å2-2.19 Å2
2--0.54 Å20 Å2
3----2.17 Å2
Refinement stepCycle: 1 / Resolution: 2.66→42.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2993 0 56 18 3067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133200
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172728
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.6834357
X-RAY DIFFRACTIONr_angle_other_deg1.0771.6036364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6015375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.58822.872188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59415484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3151516
X-RAY DIFFRACTIONr_chiral_restr0.0410.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023637
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02705
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_it1.9644.6541497
X-RAY DIFFRACTIONr_mcbond_other1.9644.6531496
X-RAY DIFFRACTIONr_mcangle_it3.4686.9621873
X-RAY DIFFRACTIONr_mcangle_other3.4676.9631874
X-RAY DIFFRACTIONr_scbond_it1.5964.7961702
X-RAY DIFFRACTIONr_scbond_other1.5964.7961703
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.897.1412479
X-RAY DIFFRACTIONr_long_range_B_refined6.1851.9443409
X-RAY DIFFRACTIONr_long_range_B_other6.17951.9473410
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5981 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.66→2.729 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 60 -
Rwork0.385 955 -
obs--95.57 %

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