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- PDB-8ru3: Crystal structure of beta-catenin in complex with alpha-helical p... -

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Basic information

Entry
Database: PDB / ID: 8ru3
TitleCrystal structure of beta-catenin in complex with alpha-helical peptide inhibitor
Components
  • Axin-1
  • Catenin beta-1
KeywordsSIGNALING PROTEIN / Peptidometic inhibitor of Catenin Beta-1
Function / homology
Function and homology information


beta-catenin destruction complex assembly / armadillo repeat domain binding / 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 destruction complex assembly / armadillo repeat domain binding / 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 / Binding of TCF/LEF:CTNNB1 to target gene promoters / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / central nervous system vasculogenesis / regulation of centriole-centriole cohesion / head development / RUNX3 regulates WNT signaling / regulation of centromeric sister chromatid cohesion / Regulation of CDH11 function / embryonic axis specification / Specification of the neural plate border / cell development / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / lens morphogenesis in camera-type eye / beta-catenin-TCF complex / endodermal cell fate commitment / 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 / axial mesoderm formation / establishment of blood-retinal barrier / dorsal/ventral axis specification / sympathetic ganglion development / fungiform papilla formation / positive regulation of endothelial cell differentiation / 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 / 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 / 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 / activation of protein kinase activity / apicolateral plasma membrane / 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 / Formation of definitive endoderm / regulation of smooth muscle cell proliferation / post-anal tail morphogenesis / epithelial cell proliferation involved in prostate gland development / embryonic brain development / catenin complex / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding
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 / DIX domain / RGS, subdomain 1/3 / DIX domain superfamily / DIX domain / DIX domain 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 / Beta-catenin / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / 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
Similarity search - Domain/homology
Axin-1 / Catenin beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsYeste Vazquez, A. / Klintrot, C.I.R. / Grossmann, T.N. / Hennig, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Structure-Based Design of Bicyclic Helical Peptides That Target the Oncogene beta-Catenin.
Authors: Yeste-Vazquez, A. / Paulussen, F.M. / Wendt, M. / Klintrot, R. / Schulte, C. / Wallraven, K. / van Gijzel, L. / Simeonov, B. / van der Gaag, M. / Gerber, A. / Maric, H.M. / Hennig, S. / Grossmann, T.N.
History
DepositionJan 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catenin beta-1
P: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8945
Polymers59,7872
Non-polymers1063
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-42 kcal/mol
Surface area22320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.526, 91.255, 112.984
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Catenin beta-1 / Beta-catenin


Mass: 58236.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 134-665 Catenin beta-1 / Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNB1, CTNNB, OK/SW-cl.35, PRO2286 / Plasmid: pGEX / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35222
#2: Protein/peptide Axin-1 / Axis inhibition protein 1 / hAxin


Mass: 1550.737 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: AC-GESIDEHLQRVW-NH2 / Source: (synth.) Homo sapiens (human) / References: UniProt: O15169
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.03 Å3/Da / Density % sol: 39.6 % / Description: Rod shaped
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: Crystals grown in 100 mM NaKPO4, 2M NaCl.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.001→71.013 Å / Num. obs: 18536 / % possible obs: 93.5 % / Observed criterion σ(I): 1 / Redundancy: 52 % / Biso Wilson estimate: 36.8 Å2 / CC1/2: 1 / Rpim(I) all: 0.03 / Net I/σ(I): 11.6
Reflection shellResolution: 2.002→2.207 Å / Redundancy: 30.9 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 926 / CC1/2: 0.958 / Rpim(I) all: 0.124 / % possible all: 61.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Cootmodel building
PHASERphasing
STARANISOdata scaling
xia2.multiplexdata reduction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.001→70.991 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.162 / SU B: 6.8 / SU ML: 0.174 / Average fsc free: 0.9573 / Average fsc work: 0.9717 / Cross valid method: FREE R-VALUE / ESU R: 0.899 / ESU R Free: 0.283
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 935 5.045 %RANDOM
Rwork0.1839 17600 --
all0.186 ---
obs-18535 52.451 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.859 Å2
Baniso -1Baniso -2Baniso -3
1-0.276 Å2-0 Å20 Å2
2--0.34 Å2-0 Å2
3----0.616 Å2
Refinement stepCycle: LAST / Resolution: 2.001→70.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3976 0 3 125 4104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0124056
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164046
X-RAY DIFFRACTIONr_angle_refined_deg0.9211.835507
X-RAY DIFFRACTIONr_angle_other_deg0.2861.7479268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4195520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.989530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.94110727
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.55610166
X-RAY DIFFRACTIONr_chiral_restr0.0370.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024787
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02881
X-RAY DIFFRACTIONr_nbd_refined0.190.21019
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.23730
X-RAY DIFFRACTIONr_nbtor_refined0.1580.22038
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.22112
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2116
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1370.215
X-RAY DIFFRACTIONr_nbd_other0.150.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1170.23
X-RAY DIFFRACTIONr_mcbond_it2.6873.9162086
X-RAY DIFFRACTIONr_mcbond_other2.6823.9152085
X-RAY DIFFRACTIONr_mcangle_it4.0347.0472606
X-RAY DIFFRACTIONr_mcangle_other4.0277.0472606
X-RAY DIFFRACTIONr_scbond_it3.9854.5381970
X-RAY DIFFRACTIONr_scbond_other3.9844.5381971
X-RAY DIFFRACTIONr_scangle_it6.2858.1012901
X-RAY DIFFRACTIONr_scangle_other6.2848.1012902
X-RAY DIFFRACTIONr_lrange_it8.36348.15517313
X-RAY DIFFRACTIONr_lrange_other8.36348.16917282
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.001-2.0530.53820.29340.30125620.9470.9171.40520.29
2.053-2.1090.43370.2961500.30124880.8540.9266.31030.29
2.109-2.170.236250.2683900.26624680.9560.9416.81520.262
2.17-2.2370.353440.2575790.26323570.9120.95426.43190.241
2.237-2.310.272370.2347240.23623010.9560.95933.07260.21
2.31-2.3910.252430.2288210.22922310.9550.96538.7270.197
2.391-2.4810.278370.2239100.22621690.9490.96843.66070.189
2.481-2.5820.276560.2429380.24420580.9520.96348.29930.209
2.582-2.6970.338650.23510040.24119960.9270.96453.55710.199
2.697-2.8290.27640.22810900.2319100.9540.96560.41880.191
2.829-2.9810.271650.21911770.22118170.9590.96968.35440.181
2.981-3.1620.248660.2112520.21217420.9640.97275.66020.169
3.162-3.380.262750.21113300.21416350.9520.97285.93270.182
3.38-3.650.244750.19913970.20115260.9640.97496.46130.168
3.65-3.9970.24770.16913310.17314080.9630.981000.142
3.997-4.4670.162590.1412240.14112830.9850.9881000.129
4.467-5.1550.153390.14211050.14311440.990.9891000.133
5.155-6.3050.221450.1949420.1959870.980.9791000.178
6.305-8.8820.194320.147450.1417770.9820.9871000.147
8.882-70.9910.218220.174570.1724790.9570.9821000.201

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