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- PDB-1th1: Beta-catenin in complex with a phosphorylated APC 20aa repeat fragment -

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Basic information

Entry
Database: PDB / ID: 1th1
TitleBeta-catenin in complex with a phosphorylated APC 20aa repeat fragment
Components
  • Adenomatous polyposis coli protein
  • Beta-catenin
KeywordsCELL ADHESION/ANTITUMOR PROTEIN / protein-protein complex / CELL ADHESION-ANTITUMOR PROTEIN COMPLEX
Function / homology
Function and homology information


APC truncation mutants are not K63 polyubiquitinated / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / beta-catenin-ICAT complex ...APC truncation mutants are not K63 polyubiquitinated / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / beta-catenin-ICAT complex / CDH11 homotypic and heterotypic interactions / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / neural plate development / metanephros morphogenesis / glial cell fate determination / Regulation of CDH19 Expression and Function / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / oviduct development / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / regulation of timing of anagen / negative regulation of mitotic cell cycle, embryonic / regulation of microtubule-based movement / Binding of TCF/LEF:CTNNB1 to target gene promoters / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / central nervous system vasculogenesis / negative regulation of cell cycle G1/S phase transition / regulation of centriole-centriole cohesion / RUNX3 regulates WNT signaling / regulation of centromeric sister chromatid cohesion / Regulation of CDH11 function / embryonic axis specification / Specification of the neural plate border / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / lens morphogenesis in camera-type eye / beta-catenin-TCF complex / endodermal cell fate commitment / gamma-catenin binding / acinar cell differentiation / dorsal root ganglion development / synaptic vesicle clustering / positive regulation of fibroblast growth factor receptor signaling pathway / proximal/distal pattern formation / neuron fate determination / layer formation in cerebral cortex / Formation of the nephric duct / positive regulation of myoblast proliferation / establishment of blood-retinal barrier / regulation of attachment of spindle microtubules to kinetochore / dorsal/ventral axis specification / sympathetic ganglion development / fungiform papilla formation / positive regulation of endothelial cell differentiation / positive regulation of pseudopodium assembly / negative regulation of cyclin-dependent protein serine/threonine kinase activity / presynaptic active zone cytoplasmic component / mesenchymal to epithelial transition / embryonic foregut morphogenesis / hindbrain development / lung epithelial cell differentiation / positive regulation of determination of dorsal identity / positive regulation of skeletal muscle tissue development / ectoderm development / regulation of protein localization to cell surface / hair cell differentiation / cellular response to indole-3-methanol / detection of muscle stretch / mesenchymal stem cell differentiation / smooth muscle cell differentiation / positive regulation of odontoblast differentiation / positive regulation of protein localization to centrosome / endothelial tube morphogenesis / mesenchymal cell proliferation involved in lung development / midbrain dopaminergic neuron differentiation / positive regulation of homotypic cell-cell adhesion / histone methyltransferase binding / alpha-catenin binding / cranial skeletal system development / regulation of calcium ion import / bicellular tight junction assembly / Germ layer formation at gastrulation / establishment of blood-brain barrier / negative regulation of oligodendrocyte differentiation / fascia adherens / epithelial cell differentiation involved in prostate gland development / flotillin complex / apicolateral plasma membrane / pattern specification process / regulation of epithelial to mesenchymal transition / positive regulation of epithelial cell proliferation involved in prostate gland development / male genitalia development / cell-cell adhesion mediated by cadherin / negative regulation of microtubule depolymerization / Formation of definitive endoderm / regulation of smooth muscle cell proliferation / epithelial cell proliferation involved in prostate gland development
Similarity search - Function
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 ...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 / 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 / Coiled-coil N-terminus of APC, dimerisation domain / Adenomatous polyposis coli (APC) repeat / Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Adenomatous polyposis coli protein / Catenin beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsXing, Y. / Clements, W.K. / Le Trong, I. / Hinds, T.R. / Stenkamp, R. / Kimelman, D. / Xu, W.
CitationJournal: Mol.Cell / Year: 2004
Title: Crystal Structure of a beta-Catenin/APC Complex Reveals a Critical Role for APC Phosphorylation in APC Function.
Authors: Xing, Y. / Clements, W.K. / Le Trong, I. / Hinds, T.R. / Stenkamp, R. / Kimelman, D. / Xu, W.
History
DepositionMay 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-catenin
B: Beta-catenin
C: Adenomatous polyposis coli protein
D: Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)155,2454
Polymers155,2454
Non-polymers00
Water82946
1
A: Beta-catenin
C: Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)77,6222
Polymers77,6222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-25 kcal/mol
Surface area24690 Å2
MethodPISA
2
B: Beta-catenin
D: Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)77,6222
Polymers77,6222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-26 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.159, 133.800, 82.166
Angle α, β, γ (deg.)90.00, 110.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-catenin / PRO2286


Mass: 58096.352 Da / Num. of mol.: 2 / Fragment: armadillo repeat
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNB1, CTNNB / Plasmid: pGEX4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P35222
#2: Protein Adenomatous polyposis coli protein / APC protein


Mass: 19526.000 Da / Num. of mol.: 2 / Fragment: phosphorylated 20 amino acid repeat
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APC, DP2.5 / Plasmid: pGEX4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* / References: UniProt: P25054
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Tris, sidium chloride, PEG2000MME, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 59245 / Num. obs: 59245 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 41.8 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 24.6
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 7 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.7 / Num. unique all: 8464 / Rsym value: 0.795 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QZ7

1qz7


Resolution: 2.5→47.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 484398.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2580 5.1 %RANDOM
Rwork0.225 ---
obs-50571 85.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.301285 e/Å3
Displacement parametersBiso mean: 49.7 Å2
Baniso -1Baniso -2Baniso -3
1-11.24 Å20 Å2-8.91 Å2
2---1.56 Å20 Å2
3----9.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-50 Å
Luzzati sigma a0.36 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8621 0 0 46 8667
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d1.81
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.362
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 305 5 %
Rwork0.299 5742 -
obs--61.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEINEDIT.PARAMPROTEINEDIT.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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