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- PDB-1v18: The crystal structure of beta-catenin armadillo repeat complexed ... -

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Basic information

Entry
Database: PDB / ID: 1v18
TitleThe crystal structure of beta-catenin armadillo repeat complexed with a phosphorylated APC 20mer repeat.
Components
  • ADENOMATOUS POLYPOSIS COLI
  • BETA-CATENIN
KeywordsSIGNALING PROTEIN / SIGNALLING COMPLEX / WNT SIGNAL / BETA-CATENIN DEGRADATION COMPLEX / CELL ADHESION / TRANSCRIPTION / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


lung cell differentiation / epicardium-derived cardiac vascular smooth muscle cell differentiation / mesenchyme morphogenesis / RUNX3 regulates WNT signaling / Regulation of CDH11 function / cardiac vascular smooth muscle cell differentiation / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Beta-catenin phosphorylation cascade / APC truncation mutants are not K63 polyubiquitinated / Apoptotic cleavage of cell adhesion proteins ...lung cell differentiation / epicardium-derived cardiac vascular smooth muscle cell differentiation / mesenchyme morphogenesis / RUNX3 regulates WNT signaling / Regulation of CDH11 function / cardiac vascular smooth muscle cell differentiation / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Beta-catenin phosphorylation cascade / APC truncation mutants are not K63 polyubiquitinated / Apoptotic cleavage of cell adhesion proteins / Disassembly of the destruction complex and recruitment of AXIN to the membrane / hair cycle process / TCF dependent signaling in response to WNT / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / endoderm formation / mesenchyme development / trachea morphogenesis / Formation of the beta-catenin:TCF transactivating complex / positive regulation of epithelial cell differentiation / 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 / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / neural plate development / metanephros morphogenesis / Deactivation of the beta-catenin transactivating complex / glial cell fate determination / 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 / animal organ development / VEGFR2 mediated vascular permeability / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / central nervous system vasculogenesis / regulation of epithelial cell differentiation / negative regulation of cell cycle G1/S phase transition / regulation of centriole-centriole cohesion / Adherens junctions interactions / regulation of centromeric sister chromatid cohesion / Degradation of beta-catenin by the destruction complex / embryonic axis specification / Ca2+ pathway / RHO GTPases activate IQGAPs / morphogenesis of embryonic epithelium / lens morphogenesis in camera-type eye / Scrib-APC-beta-catenin complex / beta-catenin-TCF complex / gamma-catenin binding / acinar cell differentiation / dorsal root ganglion development / endodermal cell fate commitment / synaptic vesicle clustering / neuron fate determination / proximal/distal pattern formation / endothelial tube morphogenesis / negative regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of microtubule-based movement / ventricular compact myocardium morphogenesis / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of attachment of spindle microtubules to kinetochore / sympathetic ganglion development / dorsal/ventral axis specification / layer formation in cerebral cortex / presynaptic active zone cytoplasmic component / positive regulation of endothelial cell differentiation / fungiform papilla formation / mesenchymal to epithelial transition / hindbrain development / positive regulation of skeletal muscle tissue development / lung epithelial cell differentiation / positive regulation of pseudopodium assembly / positive regulation of determination of dorsal identity / fascia adherens / regulation of protein localization to cell surface / ectoderm development / embryonic foregut morphogenesis / cellular response to indole-3-methanol / smooth muscle cell differentiation / positive regulation of odontoblast differentiation / mesenchymal cell proliferation involved in lung development / positive regulation of protein localization to centrosome / positive regulation of myoblast proliferation / alpha-catenin binding / histone methyltransferase binding / mesenchymal cell proliferation / regulation of calcium ion import / regulation of epithelial to mesenchymal transition / cell projection membrane
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 speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHa, N.-C. / Weis, W.I.
CitationJournal: Mol.Cell / Year: 2004
Title: Mechanism of Phosphorylation-Dependent Binding of Apc to Beta-Catenin and its Role in Beta-Catenin Degradation
Authors: Ha, N.-C. / Tonozuka, T. / Stamos, J.L. / Weis, W.I.
History
DepositionApr 9, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 6, 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: ADENOMATOUS POLYPOSIS COLI


Theoretical massNumber of molelcules
Total (without water)64,2592
Polymers64,2592
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.830, 90.060, 122.810
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 BETA-CATENIN


Mass: 58844.117 Da / Num. of mol.: 1
Fragment: ARMADILLO REPEAT, REPEAT 3 OF APC, RESIDUES 134-671
Source method: isolated from a genetically manipulated source
Details: 134-671 OF BETA-CATENIN AND 1484-1528 OF HUMAN APC(ADENOMATOUS POLYPOSIS COLI) PHOSPHORYLATED BY CK1 AND GSK-3BETA
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PPROEXHTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q02248
#2: Protein/peptide ADENOMATOUS POLYPOSIS COLI / APC PROTEIN


Mass: 5414.617 Da / Num. of mol.: 1 / Fragment: RESIDUES 1482-1528
Source method: isolated from a genetically manipulated source
Details: 134-671 OF BETA-CATENIN AND 1484-1528 OF HUMAN APC(ADENOMATOUS POLYPOSIS COLI) PHOSPHORYLATED BY CK1 AND GSK-3BETA
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEXHTA / 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.: 235 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growpH: 6.5 / Details: pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 31262 / % possible obs: 97.4 % / Redundancy: 7 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 37
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 3.6 / % possible all: 85.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I7W

1i7w


Resolution: 2.1→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3114 10 %RANDOM
Rwork0.207 ---
obs0.207 28148 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.5715 Å2 / ksol: 0.376423 e/Å3
Displacement parametersBiso mean: 47.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.941 Å20 Å20 Å2
2--16.401 Å20 Å2
3----8.459 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 0 235 4430
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0057
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_scangle_it3.442.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 417 9.7 %
Rwork0.271 3869 -
obs--77.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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