[English] 日本語
Yorodumi
- PDB-5wzz: The SIAH E3 ubiquitin ligases promote Wnt/ beta-catenin signaling... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wzz
TitleThe SIAH E3 ubiquitin ligases promote Wnt/ beta-catenin signaling through mediating Wnt-induced Axin degradation
Components
  • Axin-1
  • E3 ubiquitin-protein ligase SIAH1
KeywordsLIGASE / protein complex / WNT pathway
Function / homology
Function and homology information


beta-catenin destruction complex assembly / armadillo repeat domain binding / head development / Netrin-1 signaling / cell development / axial mesoderm formation / dorsal/ventral axis specification / post-anal tail morphogenesis / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding ...beta-catenin destruction complex assembly / armadillo repeat domain binding / head development / Netrin-1 signaling / cell development / axial mesoderm formation / dorsal/ventral axis specification / post-anal tail morphogenesis / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / I-SMAD binding / positive regulation of ubiquitin-dependent protein catabolic process / epigenetic programming in the zygotic pronuclei / Wnt signalosome / ubiquitin conjugating enzyme binding / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of protein metabolic process / nucleocytoplasmic transport / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / negative regulation of fat cell differentiation / SMAD binding / positive regulation of transforming growth factor beta receptor signaling pathway / R-SMAD binding / negative regulation of transcription elongation by RNA polymerase II / lateral plasma membrane / anatomical structure morphogenesis / canonical Wnt signaling pathway / ubiquitin-like ligase-substrate adaptor activity / positive regulation of intrinsic apoptotic signaling pathway / signaling adaptor activity / cytoplasmic microtubule organization / protein serine/threonine kinase binding / axon guidance / protein serine/threonine kinase activator activity / positive regulation of protein ubiquitination / cell periphery / TCF dependent signaling in response to WNT / positive regulation of JNK cascade / Degradation of AXIN / protein catabolic process / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / protein destabilization / Degradation of beta-catenin by the destruction complex / RING-type E3 ubiquitin transferase / beta-catenin binding / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / p53 binding / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nervous system development / microtubule cytoskeleton / protein-containing complex assembly / cytoplasmic vesicle / neuron apoptotic process / ubiquitin-dependent protein catabolic process / cell cortex / spermatogenesis / molecular adaptor activity / Estrogen-dependent gene expression / in utero embryonic development / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / early endosome / Ub-specific processing proteases / protein ubiquitination / positive regulation of apoptotic process / Amyloid fiber formation / negative regulation of gene expression / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / nucleolus / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase SINA-like, animal / Seven-in-absentia protein, TRAF-like domain / : / Sina, TRAF-like domain / Sina, zinc finger / E3 ubiquitin-protein ligase sina/sinah, RING finger / Zinc finger, SIAH-type / Zinc finger SIAH-type profile. / Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain ...E3 ubiquitin-protein ligase SINA-like, animal / Seven-in-absentia protein, TRAF-like domain / : / Sina, TRAF-like domain / Sina, zinc finger / E3 ubiquitin-protein ligase sina/sinah, RING finger / Zinc finger, SIAH-type / Zinc finger SIAH-type profile. / Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / RGS, subdomain 1/3 / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / TRAF-like / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Axin-1 / E3 ubiquitin-protein ligase SIAH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 Å
AuthorsJi, L. / Jiang, B. / Jiang, X. / Charlat, O. / Chen, A. / Mickanin, C. / Bauer, A. / Xu, W. / Yan, X.-X. / Cong, F.
CitationJournal: Genes Dev. / Year: 2017
Title: The SIAH E3 ubiquitin ligases promote Wnt/ beta-catenin signaling through mediating Wnt-induced Axin degradation
Authors: Ji, L. / Jiang, B. / Jiang, X. / Charlat, O. / Chen, A. / Mickanin, C. / Bauer, A. / Xu, W. / Yan, X.-X. / Cong, F.
History
DepositionJan 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Structure summary / Category: audit_author / struct / Item: _struct.title
Revision 1.2Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 22, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase SIAH1
B: E3 ubiquitin-protein ligase SIAH1
C: E3 ubiquitin-protein ligase SIAH1
D: E3 ubiquitin-protein ligase SIAH1
E: Axin-1
F: Axin-1
G: Axin-1
H: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,05316
Polymers95,5298
Non-polymers5238
Water3,891216
1
A: E3 ubiquitin-protein ligase SIAH1
G: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0134
Polymers23,8822
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-6 kcal/mol
Surface area11120 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase SIAH1
F: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0134
Polymers23,8822
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-6 kcal/mol
Surface area10810 Å2
MethodPISA
3
C: E3 ubiquitin-protein ligase SIAH1
E: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0134
Polymers23,8822
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-11 kcal/mol
Surface area11070 Å2
MethodPISA
4
D: E3 ubiquitin-protein ligase SIAH1
H: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0134
Polymers23,8822
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-9 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.502, 86.450, 117.454
Angle α, β, γ (deg.)90.00, 98.43, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
E3 ubiquitin-protein ligase SIAH1 / Seven in absentia homolog 1 / Siah-1 / Siah-1a


Mass: 21409.508 Da / Num. of mol.: 4 / Fragment: UNP residues 93-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIAH1, HUMSIAH / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12
References: UniProt: Q8IUQ4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide
Axin-1 / Axis inhibition protein 1 / hAxin


Mass: 2472.856 Da / Num. of mol.: 4 / Fragment: UNP residues 375-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AXIN1, AXIN / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: O15169
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 25% (w/v) PEG3350, 200 mM MgCl2, 100 mM Tris-Hcl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Jun 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 92372 / % possible obs: 99.6 % / Redundancy: 6.3 % / Net I/σ(I): 30

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ca1

4ca1


Resolution: 2.103→38.728 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2084 2275 4.81 %
Rwork0.1845 --
obs0.1857 47337 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.103→38.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6288 0 8 216 6512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016441
X-RAY DIFFRACTIONf_angle_d1.3718718
X-RAY DIFFRACTIONf_dihedral_angle_d13.8192342
X-RAY DIFFRACTIONf_chiral_restr0.058959
X-RAY DIFFRACTIONf_plane_restr0.0071131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1026-2.14830.2791460.25492612X-RAY DIFFRACTION94
2.1483-2.19830.32871530.25092825X-RAY DIFFRACTION99
2.1983-2.25330.23331460.23992773X-RAY DIFFRACTION100
2.2533-2.31420.24941450.23342854X-RAY DIFFRACTION100
2.3142-2.38230.23481530.21922764X-RAY DIFFRACTION100
2.3823-2.45920.25181200.2072877X-RAY DIFFRACTION100
2.4592-2.54710.2271300.19912846X-RAY DIFFRACTION100
2.5471-2.6490.20271450.19192815X-RAY DIFFRACTION100
2.649-2.76950.22271660.19122832X-RAY DIFFRACTION100
2.7695-2.91550.21841400.18672812X-RAY DIFFRACTION99
2.9155-3.09810.22391380.19262832X-RAY DIFFRACTION100
3.0981-3.33720.20851310.17632851X-RAY DIFFRACTION100
3.3372-3.67280.17531380.16792835X-RAY DIFFRACTION99
3.6728-4.20370.20541400.16662868X-RAY DIFFRACTION100
4.2037-5.29410.15971510.15392835X-RAY DIFFRACTION99
5.2941-38.73480.23581330.19882831X-RAY DIFFRACTION97

+
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