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- PDB-5wzz: The SIAH E3 ubiquitin ligases promote Wnt/ beta-catenin signaling... -

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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 / positive regulation of ubiquitin-dependent protein catabolic process / 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 / positive regulation of ubiquitin-dependent protein catabolic process / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / beta-catenin destruction complex / epigenetic programming in the zygotic pronuclei / 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 / Wnt signalosome / ubiquitin conjugating enzyme binding / Disassembly of the destruction complex and recruitment of AXIN to the membrane / activation of protein kinase activity / nucleocytoplasmic transport / negative regulation of protein metabolic process / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / negative regulation of fat cell differentiation / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / R-SMAD binding / negative regulation of transcription elongation by RNA polymerase II / anatomical structure morphogenesis / lateral plasma membrane / canonical Wnt signaling pathway / ubiquitin-like ligase-substrate adaptor activity / protein serine/threonine kinase binding / cytoplasmic microtubule organization / positive regulation of intrinsic apoptotic signaling pathway / signaling adaptor activity / axon guidance / positive regulation of protein ubiquitination / cell periphery / TCF dependent signaling in response to WNT / positive regulation of JNK cascade / Degradation of AXIN / sensory perception of sound / protein catabolic process / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / RING-type E3 ubiquitin transferase / beta-catenin binding / protein polyubiquitination / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / microtubule cytoskeleton / ubiquitin protein ligase activity / p53 binding / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nervous system development / cell cortex / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / cytoplasmic vesicle / neuron apoptotic process / spermatogenesis / molecular adaptor activity / in utero embryonic development / Estrogen-dependent gene expression / proteasome-mediated ubiquitin-dependent protein catabolic process / amyloid fibril formation / positive regulation of protein phosphorylation / 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 / cytosol / cytoplasm
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 / TRAF-like / RGS domain superfamily / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.18 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

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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

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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

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