- PDB-3utm: Crystal structure of a mouse Tankyrase-Axin complex -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 3utm
Title
Crystal structure of a mouse Tankyrase-Axin complex
Components
Axin-1
Tankyrase-1
Keywords
TRANSFERASE/SIGNALING PROTEIN / Tankyrase / TNKS / ankryin repeat clusters / Wnt signaling / poly-ADP-ribosylation / TRANSFERASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information
protein-containing complex assembly => GO:0065003 / Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / TCF dependent signaling in response to WNT / Degradation of AXIN / armadillo repeat domain binding / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / Regulation of PTEN stability and activity / head development / Degradation of beta-catenin by the destruction complex ...protein-containing complex assembly => GO:0065003 / Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / TCF dependent signaling in response to WNT / Degradation of AXIN / armadillo repeat domain binding / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / Regulation of PTEN stability and activity / head development / Degradation of beta-catenin by the destruction complex / : / dorsal/ventral axis specification / axial mesoderm formation / genomic imprinting / cellular response to nutrient / post-anal tail morphogenesis / Ub-specific processing proteases / axial mesoderm development / beta-catenin destruction complex / positive regulation of ubiquitin-dependent protein catabolic process / I-SMAD binding / dorsal/ventral pattern formation / Wnt signalosome / regulation of canonical Wnt signaling pathway / positive regulation of ubiquitin-protein transferase activity / nucleocytoplasmic transport / NAD+ ADP-ribosyltransferase / negative regulation of protein metabolic process / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / negative regulation of fat cell differentiation / activation of protein kinase activity / negative regulation of Wnt signaling pathway / positive regulation of transforming growth factor beta receptor signaling pathway / mitotic spindle pole / negative regulation of transcription elongation by RNA polymerase II / SMAD binding / NAD+-protein ADP-ribosyltransferase activity / R-SMAD binding / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases / lateral plasma membrane / NAD+-protein poly-ADP-ribosyltransferase activity / positive regulation of protein kinase activity / mRNA transport / canonical Wnt signaling pathway / nuclear pore / signaling adaptor activity / cytoplasmic microtubule organization / positive regulation of JUN kinase activity / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / positive regulation of peptidyl-threonine phosphorylation / positive regulation of protein ubiquitination / cell periphery / positive regulation of JNK cascade / sensory perception of sound / regulation of protein phosphorylation / protein catabolic process / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / Wnt signaling pathway / protein polyubiquitination / positive regulation of protein catabolic process / : / protein transport / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / positive regulation of peptidyl-serine phosphorylation / cell cortex / histone binding / cytoplasmic vesicle / nuclear membrane / in utero embryonic development / chromosome, telomeric region / molecular adaptor activity / postsynaptic density / nuclear body / positive regulation of protein phosphorylation / cell cycle / protein domain specific binding / cell division / Golgi membrane / negative regulation of gene expression / signaling receptor binding / centrosome / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding Similarity search - Function
Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.628 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23847
3293
5 %
RANDOM
Rwork
0.20709
-
-
-
obs
0.2087
62479
99.85 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 63.174 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.74 Å2
0 Å2
-1.84 Å2
2-
-
1.51 Å2
0 Å2
3-
-
-
-1.76 Å2
Refinement step
Cycle: LAST / Resolution: 2→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5036
0
0
227
5263
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.019
5128
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.226
1.968
6937
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.103
5
655
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.212
24.529
223
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.4
15
902
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.875
15
29
X-RAY DIFFRACTION
r_chiral_restr
0.087
0.2
793
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
3831
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2→2.052 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.32
229
-
Rwork
0.303
4534
-
obs
-
-
99.75 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.479
-0.3659
0.4331
0.3235
-0.4234
0.6455
0.0186
-0.0766
0.012
-0.0313
0.041
-0.0003
0.0287
-0.0822
-0.0596
0.0562
0.0266
-0.0139
0.0538
0.0278
0.0659
58.6798
37.4194
-33.6585
2
0.0546
0.0723
0.0538
0.13
0.1939
0.5049
-0.0075
-0.0025
-0.0003
-0.015
0.0052
0.008
-0.0051
0.0434
0.0023
0.0389
0.0204
-0.0466
0.0671
-0.0501
0.0737
66.3641
37.1305
-23.0877
3
0.019
-0.0441
-0.1133
0.176
0.1416
0.9427
0.0613
0.0223
0.0046
-0.1358
-0.2523
-0.096
-0.7688
0.1245
0.191
0.6318
-0.0778
-0.1513
0.3975
0.1725
0.2924
62.4838
65.8117
-25.0748
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
316 - 635
2
X-RAY DIFFRACTION
2
B
328 - 634
3
X-RAY DIFFRACTION
3
C
18 - 78
+
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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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