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- PDB-9qjz: Crystal structure of ARC4 from human Tankyrase 2 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9qjz
TitleCrystal structure of ARC4 from human Tankyrase 2 in complex with phosphorylated peptide from human MDC1
Components
  • Mediator of DNA damage checkpoint protein 1
  • Poly [ADP-ribose] polymerase tankyrase-2
KeywordsSIGNALING PROTEIN / ANKYRIN REPEAT / PROTEIN-PROTEIN INTERACTION / SUBSTRATE RECRUITMENT / POLY(ADP-RIBOSYL)ATION / SIGNALING PROTEIN-PEPTIDE COMPLEX
Function / homology
Function and homology information


DNA replication checkpoint signaling / XAV939 stabilizes AXIN / positive regulation of telomere capping / chromatin-protein adaptor activity / protein localization to site of double-strand break / mitotic intra-S DNA damage checkpoint signaling / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region ...DNA replication checkpoint signaling / XAV939 stabilizes AXIN / positive regulation of telomere capping / chromatin-protein adaptor activity / protein localization to site of double-strand break / mitotic intra-S DNA damage checkpoint signaling / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / pericentriolar material / histone reader activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / SUMOylation of DNA damage response and repair proteins / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / TP53 Regulates Transcription of DNA Repair Genes / Degradation of AXIN / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Regulation of PTEN stability and activity / Wnt signaling pathway / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / nuclear envelope / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / chromosome / Processing of DNA double-strand break ends / chromosome, telomeric region / Ub-specific processing proteases / nuclear body / Golgi membrane / focal adhesion / DNA repair / DNA damage response / perinuclear region of cytoplasm / enzyme binding / nucleoplasm / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Regulator of Ty1 transposition protein 107 BRCT domain / BRCT domain / Ankyrin repeat / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Poly(ADP-ribose) polymerase catalytic domain ...: / Regulator of Ty1 transposition protein 107 BRCT domain / BRCT domain / Ankyrin repeat / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Mediator of DNA damage checkpoint protein 1 / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsPollock, K. / Cronin, N. / Guettler, S.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Wellcome TrustWT102360/Z/13/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/R01583X/1 United Kingdom
Cancer Research UKC47521/A16217 and C47521/A28286 United Kingdom
Wellcome Trust214311/Z/18/Z United Kingdom
The Lister Institute of Preventive Medicinen.a. United Kingdom
CitationJournal: R Soc Open Sci. / Year: 2025
Title: Phosphorylation as a candidate regulatory mechanism for effector recruitment to tankyrase.
Authors: Broadway, B.J. / Pollock, K. / Cronin, N. / Rottapel, R. / Sicheri, F. / Guettler, S.
History
DepositionMar 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 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: Poly [ADP-ribose] polymerase tankyrase-2
B: Poly [ADP-ribose] polymerase tankyrase-2
C: Mediator of DNA damage checkpoint protein 1
D: Mediator of DNA damage checkpoint protein 1


Theoretical massNumber of molelcules
Total (without water)39,7324
Polymers39,7324
Non-polymers00
Water1,02757
1
A: Poly [ADP-ribose] polymerase tankyrase-2
C: Mediator of DNA damage checkpoint protein 1


Theoretical massNumber of molelcules
Total (without water)19,8662
Polymers19,8662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly [ADP-ribose] polymerase tankyrase-2
D: Mediator of DNA damage checkpoint protein 1


Theoretical massNumber of molelcules
Total (without water)19,8662
Polymers19,8662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.957, 118.957, 48.322
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 490 or (resid 491 through 492...
d_2ens_1(chain "B" and (resid 490 through 542 or resid 544...
d_1ens_2(chain "C" and resid 947 through 955)
d_2ens_2(chain "D" and resid 947 through 955)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1SERSERVALVALAA490 - 5428 - 60
d_12ens_1TYRTYRLEULEUAA544 - 54662 - 64
d_13ens_1HISHISLEULEUAA548 - 64366 - 161
d_21ens_1SERSERVALVALBB490 - 5428 - 60
d_22ens_1TYRTYRLEULEUBB544 - 54662 - 64
d_23ens_1HISHISLEULEUBB548 - 64366 - 161
d_11ens_2GLNGLNSEPSEPCC947 - 9555 - 13
d_21ens_2GLNGLNSEPSEPDD947 - 9555 - 13

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.0642225756977, -0.414375553682, -0.907837188752), (-0.405556815827, -0.820366699408, 0.403140357244), (-0.911810906881, 0.39407027167, -0.115366767655)-35.0889839261, 8.46453794621, -38.9591338711
2given(-0.0745502333118, -0.428826643307, -0.900305488544), (-0.441855186771, -0.795151649742, 0.415328602237), (-0.893983364855, 0.428767493989, -0.130200535564)-35.2036284809, 6.25367893256, -39.2076273542

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Components

#1: Protein Poly [ADP-ribose] polymerase tankyrase-2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / Protein ...ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / Protein poly-ADP-ribosyltransferase tankyrase-2 / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose polymerase 2 / Tankyrase II / Tankyrase-2 / TANK2 / Tankyrase-like protein / Tankyrase-related protein


Mass: 17995.311 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: pETM30-2-TNKS2(488-649) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Protein/peptide Mediator of DNA damage checkpoint protein 1 / Nuclear factor with BRCT domains 1


Mass: 1870.737 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14676
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.75 Å3/Da / Density % sol: 55.2 % / Description: needles
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Na cacodylate pH 6.5, 0.2 M Na acetate, 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97795 Å / Relative weight: 1
ReflectionResolution: 2.31→29.74 Å / Num. obs: 17376 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 33.32 Å2 / CC1/2: 0.941 / Rmerge(I) obs: 0.787 / Rpim(I) all: 0.259 / Rrim(I) all: 0.829 / Net I/σ(I): 7
Reflection shellResolution: 2.31→2.39 Å / Redundancy: 9.2 % / Rmerge(I) obs: 5.785 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1688 / CC1/2: 0.319 / Rpim(I) all: 2.017 / Rrim(I) all: 6.129 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Aimless0.5.1data scaling
XDS01 May 2016data reduction
PHENIX2.7.15phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→29.74 Å / SU ML: 0.1982 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1909
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.225 860 5.07 %
Rwork0.185 16096 -
obs0.1871 16956 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.59 Å2
Refinement stepCycle: LAST / Resolution: 2.31→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 0 57 2573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052574
X-RAY DIFFRACTIONf_angle_d0.72183490
X-RAY DIFFRACTIONf_chiral_restr0.0471396
X-RAY DIFFRACTIONf_plane_restr0.0069456
X-RAY DIFFRACTIONf_dihedral_angle_d17.614936
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.706578597571
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS1.33699544905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.450.33161270.26452408X-RAY DIFFRACTION88.82
2.45-2.640.27171570.22262653X-RAY DIFFRACTION97.33
2.64-2.910.30581460.2462716X-RAY DIFFRACTION99.83
2.91-3.330.22341520.19712721X-RAY DIFFRACTION99.93
3.33-4.190.19941320.16072765X-RAY DIFFRACTION100
4.2-29.740.17751460.14982833X-RAY DIFFRACTION100

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