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- PDB-7lun: Human PARP14 (ARTD8), catalytic fragment in complex with RBN011980 -

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Basic information

Entry
Database: PDB / ID: 7lun
TitleHuman PARP14 (ARTD8), catalytic fragment in complex with RBN011980
ComponentsProtein mono-ADP-ribosyltransferase PARP14
KeywordsTRANSFERASE/Inhibitor / PARP14 / ARTD8 / monoPARP / ADP ribosylation / inhibitor complex / TRANSFERASE-Inhibitor complex / TRANSFERASE
Function / homology
Function and homology information


negative regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-4-mediated signaling pathway / : / Maturation of nucleoprotein / Maturation of nucleoprotein / positive regulation of tyrosine phosphorylation of STAT protein / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein mono-ADP-ribosyltransferase activity ...negative regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-4-mediated signaling pathway / : / Maturation of nucleoprotein / Maturation of nucleoprotein / positive regulation of tyrosine phosphorylation of STAT protein / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein mono-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / innate immune response / enzyme binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
PARP-14, RNA recognition motif 2 / : / : / : / : / : / : / : / : / Parp14 WWE domain ...PARP-14, RNA recognition motif 2 / : / : / : / : / : / : / : / : / Parp14 WWE domain / PARP14, first type I KH domain / PARP14, second RRM domain / PARP14, second type I KH domain / PARP14, third type I KH domain / PARP14, fourth type I KH domain / PARP14, fifth type I KH domain / PARP14, sixth type I KH domain / : / PAR14-like, first RRM domain / PARP14, third RRM domain / : / PARP14-like, eighth type I KH 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. / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Chem-YFG / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.57 Å
AuthorsDorsey, B.W. / Swinger, K.K. / Schenkel, L.B. / Church, W.D. / Perl, N.R. / Vasbinder, M.M. / Wigle, T.J. / Kuntz, K.W.
CitationJournal: Chembiochem / Year: 2021
Title: Targeted Degradation of PARP14 Using a Heterobifunctional Small Molecule.
Authors: Wigle, T.J. / Ren, Y. / Molina, J.R. / Blackwell, D.J. / Schenkel, L.B. / Swinger, K.K. / Kuplast-Barr, K. / Majer, C.R. / Church, W.D. / Lu, A.Z. / Mo, J. / Abo, R. / Cheung, A. / Dorsey, B. ...Authors: Wigle, T.J. / Ren, Y. / Molina, J.R. / Blackwell, D.J. / Schenkel, L.B. / Swinger, K.K. / Kuplast-Barr, K. / Majer, C.R. / Church, W.D. / Lu, A.Z. / Mo, J. / Abo, R. / Cheung, A. / Dorsey, B.W. / Niepel, M. / Perl, N.R. / Vasbinder, M.M. / Keilhack, H. / Kuntz, K.W.
History
DepositionFeb 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein mono-ADP-ribosyltransferase PARP14
B: Protein mono-ADP-ribosyltransferase PARP14
C: Protein mono-ADP-ribosyltransferase PARP14
D: Protein mono-ADP-ribosyltransferase PARP14
E: Protein mono-ADP-ribosyltransferase PARP14
F: Protein mono-ADP-ribosyltransferase PARP14
G: Protein mono-ADP-ribosyltransferase PARP14
H: Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,73219
Polymers177,3818
Non-polymers3,35211
Water7,296405
1
A: Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5642
Polymers22,1731
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5642
Polymers22,1731
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5642
Polymers22,1731
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5642
Polymers22,1731
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6003
Polymers22,1731
Non-polymers4272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6563
Polymers22,1731
Non-polymers4842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5642
Polymers22,1731
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Protein mono-ADP-ribosyltransferase PARP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6563
Polymers22,1731
Non-polymers4842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.990, 153.660, 87.460
Angle α, β, γ (deg.)90.000, 108.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
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: 22172.574 Da / Num. of mol.: 8
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-YFG / 7-(cyclopentylamino)-5-fluoro-2-{[(trans-4-hydroxycyclohexyl)sulfanyl]methyl}quinazolin-4(3H)-one


Mass: 391.503 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H26FN3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 48.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Acetate pH 4.5, 3.0 M Sodium Chloride, 0.2% w/v 2,2'-Thiodiglycolic acid, 0.2% w/v Adipic acid, 0.2% w/v Benzoic acid, 0.2% w/v Oxalic acid anhydrous, 0.2% w/v Terephthalic ...Details: 0.1 M Sodium Acetate pH 4.5, 3.0 M Sodium Chloride, 0.2% w/v 2,2'-Thiodiglycolic acid, 0.2% w/v Adipic acid, 0.2% w/v Benzoic acid, 0.2% w/v Oxalic acid anhydrous, 0.2% w/v Terephthalic acid, 0.02 M HEPES sodium pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.57→48.53 Å / Num. obs: 52396 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 6.5
Reflection shellResolution: 2.57→2.65 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2 / Num. unique obs: 4540 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3smj

3smj


Resolution: 2.57→48.53 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.867 / SU B: 15.618 / SU ML: 0.331 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2784 2765 5.3 %RANDOM
Rwork0.2321 ---
obs0.2346 49602 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 194.55 Å2 / Biso mean: 38.306 Å2 / Biso min: 0.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å2-1.18 Å2
2---0.13 Å20 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 2.57→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12024 0 229 405 12658
Biso mean--32.14 29.23 -
Num. residues----1488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01312700
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710858
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.68417301
X-RAY DIFFRACTIONr_angle_other_deg1.2641.60425336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08651496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33522.857735
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.102151896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2631564
X-RAY DIFFRACTIONr_chiral_restr0.0710.21592
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214410
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022782
LS refinement shellResolution: 2.57→2.637 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 186 -
Rwork0.319 3688 -
all-3874 -
obs--99.97 %

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