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- PDB-1dk8: CRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN -

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Basic information

Entry
Database: PDB / ID: 1dk8
TitleCRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN
ComponentsAXINAXIN1
KeywordsSIGNALING PROTEIN / ALPHA-HELIX / PI-HELIX
Function / homology
Function and homology information


armadillo repeat domain binding / head development / cell development / dorsal/ventral axis specification / axial mesoderm formation / post-anal tail morphogenesis / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / epigenetic programming in the zygotic pronuclei ...armadillo repeat domain binding / head development / cell development / dorsal/ventral axis specification / axial mesoderm formation / post-anal tail morphogenesis / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / epigenetic programming in the zygotic pronuclei / beta-catenin destruction complex / positive regulation of ubiquitin-dependent protein catabolic process / 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 / negative regulation of protein metabolic process / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / nucleocytoplasmic transport / negative regulation of fat cell differentiation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / negative regulation of transcription elongation by RNA polymerase II / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / activation of protein kinase activity / R-SMAD binding / ubiquitin-like ligase-substrate adaptor activity / canonical Wnt signaling pathway / lateral plasma membrane / signaling adaptor activity / cytoplasmic microtubule organization / positive regulation of peptidyl-threonine phosphorylation / positive regulation of protein ubiquitination / TCF dependent signaling in response to WNT / cell periphery / Degradation of AXIN / sensory perception of sound / positive regulation of JNK cascade / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / beta-catenin binding / protein polyubiquitination / positive regulation of protein catabolic process / : / microtubule cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / positive regulation of peptidyl-serine phosphorylation / cell cortex / cytoplasmic vesicle / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / Estrogen-dependent gene expression / in utero embryonic development / molecular adaptor activity / Ub-specific processing proteases / positive regulation of protein phosphorylation / negative regulation of gene expression / apoptotic process / ubiquitin protein ligase binding / nucleolus / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / DIX domain / DIX domain superfamily / DIX domain ...Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / RGS, subdomain 1/3 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Axin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.57 Å
AuthorsSpink, K.E. / Polakis, P. / Weis, W.I.
CitationJournal: EMBO J. / Year: 2000
Title: Structural basis of the Axin-adenomatous polyposis coli interaction.
Authors: Spink, K.E. / Polakis, P. / Weis, W.I.
History
DepositionDec 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,98513
Polymers16,7941
Non-polymers1,19112
Water3,207178
1
A: AXIN
hetero molecules

A: AXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,97026
Polymers33,5882
Non-polymers2,38224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x+1/2,-y+1/2,-z+11
Unit cell
Length a, b, c (Å)32.570, 117.880, 81.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-603-

GOL

21A-605-

GOL

31A-605-

GOL

Detailsfull-length Axin exists as a dimer in vivo

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Components

#1: Protein AXIN / AXIN1


Mass: 16794.104 Da / Num. of mol.: 1 / Fragment: RGS-HOMOLOGOUS DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: O15169
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.25
Details: sodium acetate, ammonium sulfate, glycerol, dithiothreitol, pH 4.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlAxin-RGS1drop
21.6 Mammonium sulfate1reservoir
375 mM1reservoirNaOAc
45 %glycerol1reservoir
54 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 24, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.57→29.3 Å / Num. all: 22567 / Num. obs: 22359 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.5
Reflection shellResolution: 1.57→1.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.186 / Num. unique all: 688 / % possible all: 99.1
Reflection shell
*PLUS
% possible obs: 99.1 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.57→29.3 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1491306.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2211 9.9 %RANDOM
Rwork0.172 ---
obs0.172 22338 98.9 %-
all-22567 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.91 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso mean: 15.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--1.33 Å20 Å2
3----0.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.57→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 68 178 1425
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it2.443
X-RAY DIFFRACTIONc_scangle_it3.423.5
LS refinement shellResolution: 1.57→1.67 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.216 321 8.9 %
Rwork0.185 3296 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

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