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- PDB-3se2: Human poly(ADP-ribose) polymerase 14 (PARP14/ARTD8) - catalytic d... -

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Basic information

Entry
Database: PDB / ID: 3se2
TitleHuman poly(ADP-ribose) polymerase 14 (PARP14/ARTD8) - catalytic domain in complex with 6(5H)-phenanthridinone
ComponentsPoly [ADP-ribose] polymerase 14
KeywordsTRANSFERASE / DIPHTHERIA TOXIN LIKE FOLD / NAD+ / ADP-RIBOSYLATION / Structural Genomics / Structural Genomics Consortium / SGC
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. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
3-aminobenzamide / phenanthridin-6(5H)-one / THIOCYANATE ION / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKarlberg, T. / Schutz, P. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Graslund, S. / Kouznetsova, E. ...Karlberg, T. / Schutz, P. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Graslund, S. / Kouznetsova, E. / Moche, M. / Nordlund, P. / Nyman, T. / Thorsell, A.G. / Tresaugues, L. / Weigelt, J. / Siponen, M.I. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Biotechnol. / Year: 2012
Title: Family-wide chemical profiling and structural analysis of PARP and tankyrase inhibitors.
Authors: Wahlberg, E. / Karlberg, T. / Kouznetsova, E. / Markova, N. / Macchiarulo, A. / Thorsell, A.G. / Pol, E. / Frostell, A. / Ekblad, T. / Oncu, D. / Kull, B. / Robertson, G.M. / Pellicciari, R. ...Authors: Wahlberg, E. / Karlberg, T. / Kouznetsova, E. / Markova, N. / Macchiarulo, A. / Thorsell, A.G. / Pol, E. / Frostell, A. / Ekblad, T. / Oncu, D. / Kull, B. / Robertson, G.M. / Pellicciari, R. / Schuler, H. / Weigelt, J.
History
DepositionJun 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2012Group: Database references
Revision 1.3Mar 21, 2012Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.6Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,75117
Polymers88,4744
Non-polymers1,27613
Water2,720151
1
A: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4984
Polymers22,1191
Non-polymers3793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3723
Polymers22,1191
Non-polymers2532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4405
Polymers22,1191
Non-polymers3224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4405
Polymers22,1191
Non-polymers3224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Poly [ADP-ribose] polymerase 14
C: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9389
Polymers44,2372
Non-polymers7017
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-20 kcal/mol
Surface area17440 Å2
MethodPISA
6
B: Poly [ADP-ribose] polymerase 14
D: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8128
Polymers44,2372
Non-polymers5756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-19 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.372, 82.372, 434.478
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / 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: 5 / Auth seq-ID: 1532 - 1720 / Label seq-ID: 5 - 193

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 22118.590 Da / Num. of mol.: 4 / Fragment: Catalytic domain
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

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Non-polymers , 6 types, 164 molecules

#2: Chemical ChemComp-LDR / phenanthridin-6(5H)-one


Mass: 195.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H9NO
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-3AB / 3-aminobenzamide


Mass: 136.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2O
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG3350, 0.2M KSCN, 0.1M Bis-Tris-Propane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 2, 2009 / Details: mirrors and double crystal monochromator
RadiationMonochromator: Si-111 (double crystal) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / Num. all: 40412 / Num. obs: 40412 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Rmerge(I) obs: 0.111 / Rsym value: 0.166 / Net I/σ(I): 15.7
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.416 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GOY

3goy


Resolution: 2.3→34.57 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.887 / SU B: 6.918 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25464 2021 5 %RANDOM
Rwork0.20781 ---
obs0.21014 38391 100 %-
all-38391 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.994 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å2-0.44 Å20 Å2
2---0.88 Å20 Å2
3---1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6051 0 85 151 6287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226309
X-RAY DIFFRACTIONr_bond_other_d0.0040.024199
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.9348567
X-RAY DIFFRACTIONr_angle_other_deg0.8663.00110157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8055745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57724.079331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11415955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.331532
X-RAY DIFFRACTIONr_chiral_restr0.0780.2879
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217104
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021354
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_it0.5781.53758
X-RAY DIFFRACTIONr_mcbond_other0.1391.51495
X-RAY DIFFRACTIONr_mcangle_it1.09326075
X-RAY DIFFRACTIONr_scbond_it1.55132551
X-RAY DIFFRACTIONr_scangle_it2.5724.52492
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1083medium positional0.490.5
B1083medium positional0.510.5
C1083medium positional0.520.5
D1083medium positional0.460.5
A1409loose positional0.795
B1409loose positional0.875
C1409loose positional0.945
D1409loose positional0.85
A1083medium thermal0.672
B1083medium thermal0.562
C1083medium thermal0.592
D1083medium thermal0.62
A1409loose thermal0.710
B1409loose thermal0.6110
C1409loose thermal0.6110
D1409loose thermal0.710
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 144 -
Rwork0.246 2737 -
obs--100 %

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