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- PDB-8heo: Crystal structure of SIAH1 SBD bound to Axin2 peptide -

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Basic information

Entry
Database: PDB / ID: 8heo
TitleCrystal structure of SIAH1 SBD bound to Axin2 peptide
Components
  • E3 ubiquitin-protein ligase SIAH1
  • Peptide from Axin-2
KeywordsLIGASE / E3 ubiquitin ligase / SIAH1 / Axin2 / Wnt pathway
Function / homology
Function and homology information


regulation of mismatch repair / regulation of chondrocyte development / chondrocyte differentiation involved in endochondral bone morphogenesis / intramembranous ossification / secondary heart field specification / maintenance of DNA repeat elements / Binding of TCF/LEF:CTNNB1 to target gene promoters / regulation of centromeric sister chromatid cohesion / osteoblast proliferation / Netrin-1 signaling ...regulation of mismatch repair / regulation of chondrocyte development / chondrocyte differentiation involved in endochondral bone morphogenesis / intramembranous ossification / secondary heart field specification / maintenance of DNA repeat elements / Binding of TCF/LEF:CTNNB1 to target gene promoters / regulation of centromeric sister chromatid cohesion / osteoblast proliferation / Netrin-1 signaling / cell development / negative regulation of osteoblast proliferation / mitral valve morphogenesis / dorsal/ventral axis specification / regulation of extracellular matrix organization / beta-catenin destruction complex / I-SMAD binding / mRNA stabilization / ubiquitin conjugating enzyme binding / aortic valve morphogenesis / odontogenesis / bone mineralization / anatomical structure morphogenesis / cellular response to dexamethasone stimulus / canonical Wnt signaling pathway / negative regulation of osteoblast differentiation / positive regulation of fat cell differentiation / somitogenesis / positive regulation of epithelial to mesenchymal transition / positive regulation of intrinsic apoptotic signaling pathway / axon guidance / stem cell proliferation / TCF dependent signaling in response to WNT / Degradation of AXIN / protein catabolic process / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / RING-type E3 ubiquitin transferase / protein destabilization / positive regulation of protein phosphorylation / ubiquitin-protein transferase activity / osteoblast differentiation / ubiquitin protein ligase activity / intracellular protein localization / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nervous system development / neuron apoptotic process / ubiquitin-dependent protein catabolic process / spermatogenesis / molecular adaptor activity / 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 / apoptotic process / ubiquitin protein ligase binding / centrosome / protein kinase binding / enzyme binding / 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 / 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 finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase SIAH1 / Axin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsYan, X.X. / Tian, L.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of SIAH1 SBD bound to Axin2 peptide
Authors: Yan, X.X. / Tian, L.F.
History
DepositionNov 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase SIAH1
B: E3 ubiquitin-protein ligase SIAH1
G: Peptide from Axin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2487
Polymers45,9873
Non-polymers2624
Water36020
1
A: E3 ubiquitin-protein ligase SIAH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9543
Polymers21,8231
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10500 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase SIAH1
G: Peptide from Axin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2954
Polymers24,1642
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-11 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.818, 87.932, 59.698
Angle α, β, γ (deg.)90, 101.573, 90
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 21822.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIAH1, HUMSIAH / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8IUQ4, RING-type E3 ubiquitin transferase
#2: Protein/peptide Peptide from Axin-2 / Axin-like protein / Axil / Axis inhibition protein 2 / Conductin


Mass: 2340.714 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AXIN2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y2T1
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-tris propane pH 8.0, 24% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97929 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.53→29.58 Å / Num. obs: 13846 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rpim(I) all: 0.046 / Net I/σ(I): 2.22
Reflection shellResolution: 2.53→2.59 Å / Num. unique obs: 943 / CC1/2: 0.953

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WZZ

5wzz


Resolution: 2.53→29.2 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rwork0.207 ---
obs-13846 99.9 %-
Rfree---0.263
Refinement stepCycle: LAST / Resolution: 2.53→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3025 0 4 20 3049

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