[English] 日本語
Yorodumi
- PDB-4djs: Structure of beta-catenin in complex with a stapled peptide inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4djs
TitleStructure of beta-catenin in complex with a stapled peptide inhibitor
Components
  • Catenin beta-1
  • stapled peptide RRWPQ(MK8)ILD(MK8)HVRRVWR
KeywordsSIGNALING PROTEIN/INHIBITOR / transcription regulation / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / 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 ...CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / 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 / mesenchymal stem cell differentiation / beta-catenin-ICAT complex / metanephros morphogenesis / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / neural plate development / glial cell fate determination / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / negative regulation of mitotic cell cycle, embryonic / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / oviduct development / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / regulation of timing of anagen / Binding of TCF/LEF:CTNNB1 to target gene promoters / central nervous system vasculogenesis / RUNX3 regulates WNT signaling / regulation of centriole-centriole cohesion / Regulation of CDH11 function / regulation of centromeric sister chromatid cohesion / Specification of the neural plate border / embryonic axis specification / endodermal cell fate commitment / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / dorsal root ganglion development / synaptic vesicle clustering / acinar cell differentiation / dorsal/ventral axis specification / proximal/distal pattern formation / neuron fate determination / Formation of the nephric duct / layer formation in cerebral cortex / positive regulation of myoblast proliferation / positive regulation of endothelial cell differentiation / establishment of blood-retinal barrier / sympathetic ganglion development / fungiform papilla formation / lung epithelial cell differentiation / embryonic foregut morphogenesis / hindbrain development / regulation of calcium ion import / positive regulation of skeletal muscle tissue development / positive regulation of determination of dorsal identity / ectoderm development / positive regulation of odontoblast differentiation / cranial skeletal system development / endothelial tube morphogenesis / regulation of protein localization to cell surface / hair cell differentiation / cellular response to indole-3-methanol / mesenchymal cell proliferation involved in lung development / presynaptic active zone cytoplasmic component / detection of muscle stretch / smooth muscle cell differentiation / histone methyltransferase binding / midbrain dopaminergic neuron differentiation / alpha-catenin binding / flotillin complex / establishment of blood-brain barrier / Germ layer formation at gastrulation / male genitalia development / negative regulation of oligodendrocyte differentiation / fascia adherens / epithelial cell proliferation involved in prostate gland development / apicolateral plasma membrane / embryonic brain development / Formation of definitive endoderm / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / regulation of smooth muscle cell proliferation / adherens junction assembly / beta-catenin destruction complex / oocyte development / Formation of axial mesoderm / lung-associated mesenchyme development / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of protein sumoylation / embryonic heart tube 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
Similarity search - Function
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.029 Å
AuthorsBowman, B.R. / Grossmann, T.N. / Yeh, J.T.-H. / Verdine, G.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Inhibition of oncogenic Wnt signaling through direct targeting of beta-catenin.
Authors: Grossmann, T.N. / Yeh, J.T. / Bowman, B.R. / Chu, Q. / Moellering, R.E. / Verdine, G.L.
History
DepositionFeb 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Catenin beta-1
B: stapled peptide RRWPQ(MK8)ILD(MK8)HVRRVWR


Theoretical massNumber of molelcules
Total (without water)58,8322
Polymers58,8322
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-10 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.060, 74.808, 135.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 56498.570 Da / Num. of mol.: 1 / Fragment: armadillo repeats 1-12 (UNP residues 148-665)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNB1, CTNNB, OK/SW-cl.35, PRO2286 / Production host: Escherichia coli (E. coli) / References: UniProt: P35222
#2: Protein/peptide stapled peptide RRWPQ(MK8)ILD(MK8)HVRRVWR


Mass: 2333.827 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 1.4-2.0 M sodium chloride, 100 mM Bis-Tris, 100 mM potassium phosphate monobasic, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2010
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.029→50.26 Å / Num. all: 12929 / Num. obs: 12929 / % possible obs: 99.9 %
Reflection shellHighest resolution: 3.029 Å / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.1_357)refinement
CNSrefinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.029→50.26 Å / SU ML: 0.29 / σ(F): 0.11 / Phase error: 30.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2914 1210 9.95 %
Rwork0.2633 --
obs0.266 12159 93.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.094 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-40.2095 Å2-0 Å2-0 Å2
2---18.0463 Å20 Å2
3----22.1633 Å2
Refinement stepCycle: LAST / Resolution: 3.029→50.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4007 0 0 0 4007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024067
X-RAY DIFFRACTIONf_angle_d0.4875513
X-RAY DIFFRACTIONf_dihedral_angle_d11.0221520
X-RAY DIFFRACTIONf_chiral_restr0.032670
X-RAY DIFFRACTIONf_plane_restr0.002701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.029-3.15040.33181130.337986X-RAY DIFFRACTION78
3.1504-3.29370.33961180.31961100X-RAY DIFFRACTION87
3.2937-3.46740.35291330.30951159X-RAY DIFFRACTION91
3.4674-3.68450.31831260.27731206X-RAY DIFFRACTION93
3.6845-3.96890.31431390.26281250X-RAY DIFFRACTION96
3.9689-4.36810.26891380.24921255X-RAY DIFFRACTION98
4.3681-4.99970.2631440.23261304X-RAY DIFFRACTION99
4.9997-6.29720.30531450.27471306X-RAY DIFFRACTION98
6.2972-50.26720.23441540.22771383X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.75540.10480.05171.0495-0.90952.4030.06840.44240.1678-0.3261-0.5065-0.0115-0.6875-0.3982-0.03450.6533-0.0567-0.01710.73040.09140.3518-11.218118.7504-90.3262
21.1183-1.2630.57681.774-1.18734.7313-0.07-0.1366-0.0427-0.11860.117-0.10070.1115-0.3084-0.02170.1416-0.0116-0.00390.2792-0.0030.3874-9.104214.4649-74.1386
3-1.21290.6051-0.3342.7876-0.67925.03790.1709-0.1041-0.24540.099-0.0541-0.0195-0.1176-0.4358-0.0080.11690.06160.01260.38060.09680.2996-9.636910.7068-46.529
42.3734-0.38680.881.4782-0.9931.5754-0.33810.0472-0.08210.51380.2773-0.0264-0.4039-0.13970.08330.4007-0.05690.0220.42210.05850.3694-7.61934.6017-26.3672
51.2576-0.82360.90072.2225-0.50081.0616-0.42820.132-0.03411.08490.50140.0623-0.2878-0.22030.02040.77370.0469-0.0690.34230.04670.436-0.3471-0.1264-17.3764
60.62330.6054-0.17925.3559-2.10650.9301-0.2273-0.5251-0.18552.87920.6254-1.5467-0.50250.70040.24871.2462-0.0388-0.65260.4603-0.14360.882510.38143.334-15.0264
70.22961.1527-0.03834.0107-0.15870.3151.4748-0.4876-0.84743.1155-0.5811-1.5102-0.36950.37310.19411.9138-0.0349-0.88660.5877-0.22151.055213.79646.1572-6.3697
81.56131.7215-0.57072.32940.91572.95960.0195-0.3235-0.48983.0768-0.4332-0.7969-2.69860.4833-0.43932.3857-0.2493-0.87150.29520.17650.831113.007612.0047-3.7548
91.6794-0.0638-0.87631.0796-1.1141.48610.1748-0.3150.93412.8664-1.40371.5317-1.79930.37810.01623.3847-0.2656-0.40550.5205-0.09910.51169.826520.7456-2.6184
101.32250.8251-0.18432.1351-0.50832.32921.1716-0.05010.32751.9718-0.9191.1616-1.86870.23120.10233.3934-0.4295-0.04150.7469-0.09460.78539.146922.57977.264
111.08991.18410.71234.1617-0.20321.95620.0979-0.6885-0.6201-1.17750.3233-0.55220.4849-0.4151-0.14460.6673-0.2223-0.12070.5917-0.00110.5146-15.11291.8041-65.2394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( chain A and resid 148:166 )A148 - 166
2X-RAY DIFFRACTION2( chain A and resid 167:277 )A167 - 277
3X-RAY DIFFRACTION3( chain A and resid 278:388 )A278 - 388
4X-RAY DIFFRACTION4( chain A and resid 389:443 )A389 - 443
5X-RAY DIFFRACTION5( chain A and resid 444:490 )A444 - 490
6X-RAY DIFFRACTION6( chain A and resid 491:517 )A491 - 517
7X-RAY DIFFRACTION7( chain A and resid 518:549 )A518 - 549
8X-RAY DIFFRACTION8( chain A and resid 561:603 )A561 - 603
9X-RAY DIFFRACTION9( chain A and resid 604:621 )A604 - 621
10X-RAY DIFFRACTION10( chain A and resid 622:665 )A622 - 665
11X-RAY DIFFRACTION11( chain B and resid 2:16 )B2 - 16

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more