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- PDB-1emu: STRUCTURE OF THE AXIN RGS-HOMOLOGOUS DOMAIN IN COMPLEX WITH A SAM... -

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Basic information

Entry
Database: PDB / ID: 1emu
TitleSTRUCTURE OF THE AXIN RGS-HOMOLOGOUS DOMAIN IN COMPLEX WITH A SAMP REPEAT FROM APC
Components
  • ADENOMATOUS POLYPOSIS COLI PROTEINFamilial adenomatous polyposis
  • AXINAXIN1
KeywordsSIGNALING PROTEIN / RGS domain
Function / homology
Function and homology information


APC truncation mutants are not K63 polyubiquitinated / armadillo repeat domain binding / regulation of microtubule-based movement / head development / negative regulation of cell cycle G1/S phase transition / cell development / dorsal/ventral axis specification / axial mesoderm formation / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore ...APC truncation mutants are not K63 polyubiquitinated / armadillo repeat domain binding / regulation of microtubule-based movement / head development / negative regulation of cell cycle G1/S phase transition / cell development / dorsal/ventral axis specification / axial mesoderm formation / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome / pattern specification process / bicellular tight junction assembly / protein kinase regulator activity / post-anal tail morphogenesis / negative regulation of microtubule depolymerization / negative regulation of cyclin-dependent protein serine/threonine kinase activity / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / microtubule plus-end binding / epigenetic programming in the zygotic pronuclei / beta-catenin destruction complex / positive regulation of ubiquitin-dependent protein catabolic process / regulation of microtubule-based process / heart valve development / 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 / catenin complex / I-SMAD binding / negative regulation of protein metabolic process / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cell fate specification / nucleocytoplasmic transport / endocardial cushion morphogenesis / negative regulation of fat cell differentiation / dynein complex binding / negative regulation of G1/S transition of mitotic cell cycle / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / mitotic spindle assembly checkpoint signaling / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / 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 / mitotic cytokinesis / ubiquitin-like ligase-substrate adaptor activity / bicellular tight junction / 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 / Deactivation of the beta-catenin transactivating complex / Degradation of AXIN / sensory perception of sound / adherens junction / positive regulation of JNK cascade / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / kinetochore / ruffle membrane / beta-catenin binding / Wnt signaling pathway / protein polyubiquitination / positive regulation of protein catabolic process / : / microtubule cytoskeleton / cell migration / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / lamellipodium / insulin receptor signaling pathway / positive regulation of peptidyl-serine phosphorylation / nervous system development / positive regulation of cold-induced thermogenesis / cell cortex / cytoplasmic vesicle / microtubule binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / Estrogen-dependent gene expression / in utero embryonic development / microtubule / molecular adaptor activity / Ub-specific processing proteases / cell adhesion
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 / Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions ...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 / Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Regulator of G-protein Signalling 4; domain 1 / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family / Adenomatous polyposis coli protein / Adenomatous polyposis coli, N-terminal dimerisation domain / APC, N-terminal coiled-coil domain superfamily / Adenomatous polyposis coli (APC) repeat / APC repeat / SAMP Motif / EB-1 Binding Domain / APC basic domain / APC 15 residue motif / Coiled-coil N-terminus of APC, dimerisation domain / Adenomatous polyposis coli (APC) repeat / 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 / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Axin-1 / Adenomatous polyposis coli protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 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
DepositionMar 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 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

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Assembly

Deposited unit
A: AXIN
B: ADENOMATOUS POLYPOSIS COLI PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7619
Polymers17,1172
Non-polymers6457
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-15 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.600, 69.980, 71.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AXIN / AXIN1


Mass: 15349.550 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: Bacteria (eubacteria) / References: UniProt: O15169
#2: Protein/peptide ADENOMATOUS POLYPOSIS COLI PROTEIN / Familial adenomatous polyposis


Mass: 1766.965 Da / Num. of mol.: 1 / Fragment: THIRD SAMP REPEAT / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED BY FMOC METHOD. THE SEQUENCE OF THIS PEPTIDE NATURALLY OCCURS IN HUMANS (HOMO SAPIENS)
References: UniProt: P25054
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MES, PEG 400, glycerol, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMAxin-RGS1drop
21 mMSAMP31drop
350 mMMES1reservoir
442.5 %PEG4001reservoir
515 %glycerol1reservoir
65 mMdithiothreitol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL9-210.98
SYNCHROTRONSSRL BL9-120.97
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 2, 2000
MARRESEARCH2IMAGE PLATEFeb 25, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.971
ReflectionResolution: 1.9→32 Å / Num. obs: 12617 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3 % / Rmerge(I) obs: 0.295 / Num. unique all: 611 / % possible all: 99.7
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.9→32 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 11160027.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1199 9.9 %RANDOM
Rwork0.205 ---
obs0.205 12069 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.02 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso mean: 27.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å20 Å2
2---3.13 Å20 Å2
3---4.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.9→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 42 61 1300
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it2.021.5
X-RAY DIFFRACTIONc_mcangle_it2.882
X-RAY DIFFRACTIONc_scbond_it2.722.5
X-RAY DIFFRACTIONc_scangle_it4.383
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.254 187 10.4 %
Rwork0.225 1609 -
obs--86.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
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_deg18.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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