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- PDB-3q71: Human parp14 (artd8) - macro domain 2 in complex with adenosine-5... -

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Basic information

Entry
Database: PDB / ID: 3q71
TitleHuman parp14 (artd8) - macro domain 2 in complex with adenosine-5-diphosphoribose
ComponentsPoly [ADP-ribose] polymerase 14
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / PARP14 macro 2
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+-protein poly-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+-protein poly-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 / Parp14 WWE domain / : / WWE domain superfamily / WWE domain / WWE domain profile. / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain ...PARP-14, RNA recognition motif 2 / Parp14 WWE domain / : / WWE domain superfamily / WWE domain / WWE domain profile. / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AR6 / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKarlberg, T. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Flores, A. ...Karlberg, T. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Flores, A. / Graslund, S. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Sehic, A. / Thorsell, A.G. / Tresaugues, L. / Wahlberg, E. / Weigelt, J. / Welin, M. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2013
Title: Recognition of Mono-ADP-Ribosylated ARTD10 Substrates by ARTD8 Macrodomains.
Authors: Forst, A.H. / Karlberg, T. / Herzog, N. / Thorsell, A.G. / Gross, A. / Feijs, K.L. / Verheugd, P. / Kursula, P. / Nijmeijer, B. / Kremmer, E. / Kleine, H. / Ladurner, A.G. / Schuler, H. / Luscher, B.
History
DepositionJan 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2013Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8962
Polymers24,3371
Non-polymers5591
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.350, 66.350, 110.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Poly [ADP-ribose] polymerase 14 / PARP-14 / B aggressive lymphoma protein 2


Mass: 24336.699 Da / Num. of mol.: 1 / Fragment: MACRO DOMAIN 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAL2, KIAA1268, PARP14 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: Q460N5, NAD+ ADP-ribosyltransferase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 1.4M Ammonium Sulfate, 0.1M Sodium Acetate, 0.4M Sodium Chloride, 4mM ADP-ribose, 4mM Magnesium Chloride, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.9077 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 29, 2010 / Details: mirrors
RadiationMonochromator: Bent Si (220) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9077 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 14842 / Num. obs: 14842 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.149 / Rsym value: 0.122 / Net I/σ(I): 14
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1824 / Rsym value: 0.391 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
BALBESphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IID

3iid


Resolution: 2.2→28.73 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.396 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22273 1484 10 %RANDOM
Rwork0.18731 ---
all0.19088 13357 --
obs0.19088 13357 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.088 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.34 Å20 Å2
2--0.67 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1568 0 36 88 1692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221635
X-RAY DIFFRACTIONr_bond_other_d0.0010.021093
X-RAY DIFFRACTIONr_angle_refined_deg1.2982.0022218
X-RAY DIFFRACTIONr_angle_other_deg0.833.0022673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3585202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04425.45566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.715291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.401156
X-RAY DIFFRACTIONr_chiral_restr0.070.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211764
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02294
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_it0.5871.51007
X-RAY DIFFRACTIONr_mcbond_other0.1091.5412
X-RAY DIFFRACTIONr_mcangle_it1.15521627
X-RAY DIFFRACTIONr_scbond_it1.8243628
X-RAY DIFFRACTIONr_scangle_it3.194.5591
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 107 -
Rwork0.207 971 -
obs--100 %

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