[English] 日本語
Yorodumi
- PDB-4pnm: Crystal Structure of human Tankyrase 2 in complex with Nu1025. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pnm
TitleCrystal Structure of human Tankyrase 2 in complex with Nu1025.
ComponentsTankyrase-2
KeywordsTRANSFERASE / poly(ADP-ribosylation) polymerase (PARP)
Function / homology
Function and homology information


XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity ...XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / nuclear envelope / chromosome, telomeric region / Ub-specific processing proteases / Golgi membrane / perinuclear region of cytoplasm / enzyme binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / Ankyrin repeat / 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. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. ...: / Ankyrin repeat / 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. / 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 (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
8-HYDROXY-2-METHYL-3-HYDRO-QUINAZOLIN-4-ONE / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.19 Å
AuthorsQiu, W. / Lam, R. / Romanov, V. / Gordon, R. / Gebremeskel, S. / Vodsedalek, J. / Thompson, C. / Beletskaya, I. / Battaile, K.P. / Pai, E.F. / Chirgadze, N.Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2.
Authors: Qiu, W. / Lam, R. / Voytyuk, O. / Romanov, V. / Gordon, R. / Gebremeskel, S. / Vodsedalek, J. / Thompson, C. / Beletskaya, I. / Battaile, K.P. / Pai, E.F. / Rottapel, R. / Chirgadze, N.Y.
History
DepositionMay 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tankyrase-2
B: Tankyrase-2
C: Tankyrase-2
D: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,03614
Polymers103,9454
Non-polymers1,09010
Water6,197344
1
A: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2283
Polymers25,9861
Non-polymers2422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2283
Polymers25,9861
Non-polymers2422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2904
Polymers25,9861
Non-polymers3043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2904
Polymers25,9861
Non-polymers3043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.960, 79.250, 153.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsmonomer

-
Components

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


Mass: 25986.291 Da / Num. of mol.: 4 / Fragment: PARP, catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NU1 / 8-HYDROXY-2-METHYL-3-HYDRO-QUINAZOLIN-4-ONE / NU1025


Mass: 176.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H8N2O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M NaCl, 0.1M Sodium, Hepes buffer at pH7.5, 12-15% iso-propanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→79.25 Å / Num. obs: 46699 / % possible obs: 99.9 % / Redundancy: 7.05 % / Biso Wilson estimate: 36.76 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.44 / Num. measured all: 329620
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. possibleNum. unique obsNet I/σ(I) obs% possible all
2.19-2.246.750.56242023832.8298.5
2.24-2.297.370.519281928183.45100
2.29-2.347.370.488257825763.5899.9
2.34-2.397.380.461234423433.93100
2.39-2.457.30.418260926094.36100
2.45-2.527.230.389270127014.71100
2.52-2.597.130.335240924095.28100
2.59-2.676.890.309248424835.81100
2.67-2.766.460.262246124576.599.8
2.76-2.877.090.224259825988.1100
2.87-2.996.990.182242624259.7100
2.99-3.136.690.1372364236412100
3.13-3.37.470.1172394239315.65100
3.3-3.517.380.0872340233919.92100
3.51-3.797.270.072378237824.59100
3.79-4.197.010.0562396239429.1599.9
4.19-4.826.660.0462351234633.6199.8
4.82-6.126.490.0472340233731.6499.9
6.12-79.256.810.0392354234637.2699.7

-
Processing

Software
NameVersionClassification
XDS2005/3data reduction
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.14data extraction
BUSTER2.10.0refinement
RefinementResolution: 2.19→76.92 Å / Cor.coef. Fo:Fc: 0.8968 / Cor.coef. Fo:Fc free: 0.8814 / SU R Cruickshank DPI: 0.272 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.282 / SU Rfree Blow DPI: 0.207 / SU Rfree Cruickshank DPI: 0.206
RfactorNum. reflection% reflectionSelection details
Rfree0.2437 1070 2.3 %RANDOM
Rwork0.2035 ---
obs0.2044 46616 99.82 %-
Displacement parametersBiso max: 123.09 Å2 / Biso mean: 43.63 Å2 / Biso min: 20.47 Å2
Baniso -1Baniso -2Baniso -3
1--19.2034 Å20 Å20 Å2
2--0.3555 Å20 Å2
3---18.8479 Å2
Refine analyzeLuzzati coordinate error obs: 0.291 Å
Refinement stepCycle: final / Resolution: 2.19→76.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6554 0 64 344 6962
Biso mean--36.95 48.73 -
Num. residues----815
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3094SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes152HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1029HARMONIC5
X-RAY DIFFRACTIONt_it6831HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion808SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7606SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6831HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg9196HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion3.14
LS refinement shellResolution: 2.19→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2761 82 2.45 %
Rwork0.2419 3271 -
all0.2427 3353 -
obs--99.82 %

+
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