[English] 日本語
Yorodumi
- PDB-9txv: Catalytic domain of human tankyrase 2 in complex with a dual-site... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9txv
TitleCatalytic domain of human tankyrase 2 in complex with a dual-site inhibitor
Components(Poly [ADP-ribose] polymerase tankyrase-2) x 2
KeywordsTRANSFERASE / ADP-ribosylation / Inhibitor / PARP / TNKS2
Function / homology
Function and homology information


XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / negative regulation of telomere maintenance via telomere lengthening / 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 ...XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / negative regulation of telomere maintenance via telomere lengthening / 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 / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / Wnt signaling pathway / protein polyubiquitination / Regulation of PTEN stability and activity / positive regulation of canonical Wnt signaling pathway / nuclear envelope / chromosome, telomeric region / Ub-specific processing proteases / Golgi membrane / perinuclear region of cytoplasm / enzyme binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ankyrin repeats (many copies) / 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 / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat ...Ankyrin repeats (many copies) / 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 / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
: / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPaakkonen, J. / Lehtio, L.
Funding support Finland, 1items
OrganizationGrant numberCountry
Jane and Aatos Erkko Foundation Finland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2026
Title: Replacement soaking for human tankyrase 2 enables studies on substrate analogues and inhibitors.
Authors: Paakkonen, J. / Sowa, S.T. / Bosetti, C. / Lehtio, L.
History
DepositionJan 16, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase tankyrase-2
C: Poly [ADP-ribose] polymerase tankyrase-2
B: Poly [ADP-ribose] polymerase tankyrase-2
D: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,13213
Polymers49,5784
Non-polymers1,5549
Water00
1
A: Poly [ADP-ribose] polymerase tankyrase-2
B: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5186
Polymers24,7892
Non-polymers7294
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Poly [ADP-ribose] polymerase tankyrase-2
D: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6147
Polymers24,7892
Non-polymers8255
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.79, 76.43, 149.06
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11chain A
21chain C
32chain B, fragment 1
42chain D, fragment 1
53chain B, fragment 2
63chain D, fragment 2

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
111GLYGLYPHEPHEAA952 - 11109 - 167
211GLYGLYPHEPHECB952 - 11109 - 167
322ALAALAARGARGBC1116 - 11283 - 15
422ALAALAARGARGDD1116 - 11283 - 15
533ALAALAGLUGLUBC1137 - 116124 - 48
633ALAALAGLUGLUDD1137 - 116124 - 48

NCS ensembles :
IDDetails (eV)
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

-
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: 19352.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fragment L946-M1113 of catalytic domain L946-E1161 after cleavage with chymotrypsin
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: pNIC-MBP / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Protein/peptide 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: 5436.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fragment K1114-E1161 of catalytic domain L946-E1161 after cleavage with chymotrypsin
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: pNIC-MBP / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-A1JX7 / ~{N}-(2-methoxyphenyl)-4-[[methyl-[2-(4-oxidanylidene-3~{H}-quinazolin-2-yl)ethyl]carbamoyl]amino]benzamide


Mass: 471.508 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H25N5O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 22% (w/v) PEG 3350, 0.2 M lithium sulfate, 0.1 M Tris, 1% (v/v) DMSO, 1 mM inhibitor

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.9→41.66 Å / Num. obs: 11149 / % possible obs: 99.8 % / Redundancy: 37.6 % / Biso Wilson estimate: 41.2 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.403 / Rrim(I) all: 0.409 / Net I/σ(I): 12.81
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 26.9 % / Rmerge(I) obs: 2.375 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 816 / CC1/2: 0.772 / CC star: 0.933 / Rrim(I) all: 2.421 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSJun 30, 2023data reduction
XSCALEJun 30, 2023data scaling
Coot0.9.8.93model building
PHASER2.8.3phasing
REFMAC5.8.0425refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→41.66 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.887 / SU B: 16.921 / SU ML: 0.312 / Cross valid method: FREE R-VALUE / ESU R Free: 0.442
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2557 1114 9.992 %Random selection
Rwork0.1977 10035 --
all0.204 ---
obs-11149 99.749 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.905 Å2
Baniso -1Baniso -2Baniso -3
1-2.786 Å20 Å20 Å2
2--1.956 Å2-0 Å2
3----4.742 Å2
Refinement stepCycle: LAST / Resolution: 2.9→41.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 97 0 3319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123409
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163012
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.8664591
X-RAY DIFFRACTIONr_angle_other_deg0.661.7976920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1925397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.534527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23810538
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.97210175
X-RAY DIFFRACTIONr_chiral_restr0.0660.2448
X-RAY DIFFRACTIONr_chiral_restr_other1.3030.26
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024067
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02875
X-RAY DIFFRACTIONr_nbd_refined0.2090.2614
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.22857
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21617
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21805
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.271
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.214
X-RAY DIFFRACTIONr_nbd_other0.2270.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.22
X-RAY DIFFRACTIONr_mcbond_it3.8264.6441603
X-RAY DIFFRACTIONr_mcbond_other3.8234.6441603
X-RAY DIFFRACTIONr_mcangle_it6.1778.3281995
X-RAY DIFFRACTIONr_mcangle_other6.1788.3291996
X-RAY DIFFRACTIONr_scbond_it4.1254.8221806
X-RAY DIFFRACTIONr_scbond_other4.1244.8221807
X-RAY DIFFRACTIONr_scangle_it6.5678.6872596
X-RAY DIFFRACTIONr_scangle_other6.5658.6862597
X-RAY DIFFRACTIONr_lrange_it8.85545.3373714
X-RAY DIFFRACTIONr_lrange_other8.85345.3473715
X-RAY DIFFRACTIONr_ncsr_local_group_10.0870.0521583
X-RAY DIFFRACTIONr_ncsr_local_group_20.0130.05997
X-RAY DIFFRACTIONr_ncsr_local_group_30.0090.052745
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.086820.05008
12CX-RAY DIFFRACTIONLocal ncs0.086820.05008
23BX-RAY DIFFRACTIONLocal ncs0.012590.05007
24DX-RAY DIFFRACTIONLocal ncs0.012590.05007
35BX-RAY DIFFRACTIONLocal ncs0.009260.05008
36DX-RAY DIFFRACTIONLocal ncs0.009260.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.9750.403770.321736X-RAY DIFFRACTION99.7546
2.975-3.0560.335810.298692X-RAY DIFFRACTION99.6134
3.056-3.1440.249750.242674X-RAY DIFFRACTION99.8667
3.144-3.240.319740.239685X-RAY DIFFRACTION100
3.24-3.3460.26720.193639X-RAY DIFFRACTION99.8596
3.346-3.4620.277680.212627X-RAY DIFFRACTION99.2857
3.462-3.5920.277660.195598X-RAY DIFFRACTION99.5502
3.592-3.7380.249670.196585X-RAY DIFFRACTION99.8469
3.738-3.9020.211620.178566X-RAY DIFFRACTION100
3.902-4.0910.207590.15539X-RAY DIFFRACTION99.8331
4.091-4.310.162590.144523X-RAY DIFFRACTION100
4.31-4.5690.221550.153493X-RAY DIFFRACTION100
4.569-4.880.186520.137453X-RAY DIFFRACTION99.8024
4.88-5.2650.223470.151440X-RAY DIFFRACTION99.7951
5.265-5.7580.247460.213403X-RAY DIFFRACTION99.7778
5.758-6.4220.443410.236369X-RAY DIFFRACTION100
6.422-7.3870.278370.23331X-RAY DIFFRACTION100
7.387-8.9770.254320.205287X-RAY DIFFRACTION99.6875
8.977-12.4110.259260.195239X-RAY DIFFRACTION99.6241
12.411-41.660.314180.354156X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more