[English] 日本語
Yorodumi
- PDB-6m91: Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-103... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6m91
TitleMonophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-103094 ternary complex
Components
  • Catenin beta-1
  • F-box/WD repeat-containing protein 1A
  • S-phase kinase-associated protein 1
KeywordsLIGASE / Ubiquitin Molecular Glue Enhancer
Function / homology
Function and homology information


protein phosphorylated amino acid binding / 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 ...protein phosphorylated amino acid binding / 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 / embryonic axis specification / endodermal cell fate commitment / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / positive regulation of fibroblast growth factor receptor signaling pathway / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / F-box domain binding / dorsal root ganglion development / synaptic vesicle clustering / acinar cell differentiation / dorsal/ventral axis specification / proximal/distal pattern formation / neuron fate determination / layer formation in cerebral cortex / positive regulation of myoblast proliferation / positive regulation of endothelial cell differentiation / sympathetic ganglion development / establishment of blood-retinal barrier / fungiform papilla formation / lung epithelial cell differentiation / embryonic foregut morphogenesis / hindbrain development / regulation of calcium ion import / positive regulation of determination of dorsal identity / positive regulation of skeletal muscle tissue development / ectoderm development / positive regulation of odontoblast differentiation / PcG protein complex / cranial skeletal system development / endothelial tube morphogenesis / regulation of protein localization to cell surface / hair cell differentiation / mesenchymal cell proliferation involved in lung development / detection of muscle stretch / smooth muscle cell differentiation / histone methyltransferase binding / midbrain dopaminergic neuron differentiation / presynaptic active zone cytoplasmic component / alpha-catenin binding / cellular response to indole-3-methanol / flotillin complex / Germ layer formation at gastrulation / establishment of blood-brain barrier / male genitalia development / negative regulation of oligodendrocyte differentiation / apicolateral plasma membrane / fascia adherens / epithelial cell proliferation involved in prostate gland development / 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 / ubiquitin ligase activator activity / Cul7-RING ubiquitin ligase complex / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of ubiquitin protein ligase activity / maintenance of protein location in nucleus / oocyte development / beta-catenin destruction complex / lung-associated mesenchyme development / Formation of axial mesoderm / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of circadian rhythm / negative regulation of protein sumoylation / adherens junction assembly
Similarity search - Function
D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / Monooxygenase - #50 / Beta-catenin / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation ...D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / Monooxygenase - #50 / Beta-catenin / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Monooxygenase / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Armadillo/beta-catenin-like repeats / Armadillo / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / SKP1/BTB/POZ domain superfamily / Armadillo-like helical / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-J97 / PHOSPHATE ION / Catenin beta-1 / S-phase kinase-associated protein 1 / F-box/WD repeat-containing protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsSimonetta, K.R. / Clifton, M.C. / Walter, R.L. / Ranieri, G.M. / Carter, J.J.
CitationJournal: Nat Commun / Year: 2019
Title: Prospective discovery of small molecule enhancers of an E3 ligase-substrate interaction.
Authors: Simonetta, K.R. / Taygerly, J. / Boyle, K. / Basham, S.E. / Padovani, C. / Lou, Y. / Cummins, T.J. / Yung, S.L. / von Soly, S.K. / Kayser, F. / Kuriyan, J. / Rape, M. / Cardozo, M. / Gallop, ...Authors: Simonetta, K.R. / Taygerly, J. / Boyle, K. / Basham, S.E. / Padovani, C. / Lou, Y. / Cummins, T.J. / Yung, S.L. / von Soly, S.K. / Kayser, F. / Kuriyan, J. / Rape, M. / Cardozo, M. / Gallop, M.A. / Bence, N.F. / Barsanti, P.A. / Saha, A.
History
DepositionAug 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: F-box/WD repeat-containing protein 1A
B: S-phase kinase-associated protein 1
C: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0416
Polymers69,4073
Non-polymers6343
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-49 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.490, 82.490, 111.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein F-box/WD repeat-containing protein 1A / E3RSIkappaB / Epididymis tissue protein Li 2a / F-box and WD repeats protein beta-TrCP / ...E3RSIkappaB / Epididymis tissue protein Li 2a / F-box and WD repeats protein beta-TrCP / pIkappaBalpha-E3 receptor subunit


Mass: 49418.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTRC, BTRCP, FBW1A, FBXW1A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y297
#2: Protein S-phase kinase-associated protein 1 / / Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti ...Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti protein II / OCP-II / RNA polymerase II elongation factor-like protein / SIII / Transcription elongation factor B polypeptide 1-like / p19skp1


Mass: 16459.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Escherichia coli (E. coli) / References: UniProt: P63208

-
Protein/peptide , 1 types, 1 molecules C

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


Mass: 3528.714 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P35222

-
Non-polymers , 4 types, 28 molecules

#4: Chemical ChemComp-J97 / 3-({4-[(2,6-dichlorophenyl)sulfanyl]-2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl}amino)benzoic acid


Mass: 503.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H11Cl2F3N2O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 8% PEG 4000 0.1M BTP pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→44.063 Å / Num. obs: 33157 / % possible obs: 99.5 % / Redundancy: 4.232 % / Biso Wilson estimate: 68.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.051 / Χ2: 1 / Net I/σ(I): 17.69 / Num. measured all: 140329 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.464.2471.3910.9910506248924740.3971.58999.4
2.46-2.534.2581.0611.2910117239623760.4891.21299.2
2.53-2.64.2560.7281.949784232422990.6660.83298.9
2.6-2.684.2630.5662.489702228622760.7590.64699.6
2.68-2.774.260.3873.659215217221630.890.44299.6
2.77-2.874.2650.2755.019098214921330.9390.31499.3
2.87-2.984.2580.1897.038767206520590.970.21699.7
2.98-3.14.2610.149.58314195619510.9820.1699.7
3.1-3.244.2690.09413.988171192119140.9920.10799.6
3.24-3.394.250.06319.877612179817910.9960.07299.6
3.39-3.584.2450.04825.517319172717240.9980.05599.8
3.58-3.794.2110.03931.426759160916050.9980.04599.8
3.79-4.064.2030.03335.476422152915280.9980.03899.9
4.06-4.384.1530.02940.395927142914270.9990.03399.9
4.38-4.84.1540.02644.415479132013190.9990.0399.9
4.8-5.374.1720.02545.054898117511740.9990.02899.9
5.37-6.24.1850.02643.534390104910490.9990.029100
6.2-7.594.1850.02446.5737088878860.9990.02899.9
7.59-10.734.1460.0251.4927906786730.9990.02299.3
10.73-44.0634.0210.0252.3313513703360.9990.02390.8

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.4→44.063 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2163 1245 3.76 %
Rwork0.1914 31910 -
obs0.1923 33155 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.95 Å2 / Biso mean: 84.3341 Å2 / Biso min: 45.38 Å2
Refinement stepCycle: final / Resolution: 2.4→44.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4217 0 38 25 4280
Biso mean--78.33 67.87 -
Num. residues----544
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.49610.33251460.31563542368899
2.4961-2.60970.31131400.27163519365999
2.6097-2.74730.30181400.258935603700100
2.7473-2.91940.27541440.23735363680100
2.9194-3.14470.27911400.229135363676100
3.1447-3.46110.22851310.210435783709100
3.4611-3.96160.2141270.189835733700100
3.9616-4.99020.17171420.157735333675100
4.9902-44.07050.20081350.17133533366899
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)
11.3314-0.14090.47671.92750.55120.45570.04440.18730.4129-0.0958-0.1610.09460.08590.1920.10041.05270.37940.0560.7475-0.03820.917133.5083-43.583-11.5324
23.2216-0.6705-0.08922.2841-0.15862.55140.23940.1515-0.2347-0.0171-0.1141-0.3180.18820.0022-0.11310.73740.1018-0.07530.36760.00070.613511.4421-13.4314-1.6466
33.8469-0.3228-0.59161.39750.6481.514-0.0633-0.58730.11880.5921-0.34350.79150.0191-1.27360.38170.97320.17750.37631.47150.05480.97118.8164-69.4707-9.2563
41.17350.44251.55882.2535-1.45184.06140.7452-0.13020.45630.1995-1.35960.3398-0.4309-0.66690.45041.24850.18410.36531.3238-0.15480.830418.3344-59.56114.4838
55.74831.29660.56663.26790.07591.72210.0251-0.33290.15560.9104-0.0057-0.2069-0.2824-0.3690.10631.11240.4440.10040.82670.01250.626434.0029-57.5171-5.9798
62.0224-1.1730.12841.5806-1.2515.69320.2254-0.48230.64150.4935-0.5310.0272-0.5421-0.23530.19650.9790.1247-0.04030.5074-0.03430.52387.0595-0.21663.9811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 138 through 252 )A138 - 252
2X-RAY DIFFRACTION2chain 'A' and (resid 253 through 548 )A253 - 548
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 58 )B2 - 58
4X-RAY DIFFRACTION4chain 'B' and (resid 59 through 78 )B59 - 78
5X-RAY DIFFRACTION5chain 'B' and (resid 79 through 139 )B79 - 139
6X-RAY DIFFRACTION6chain 'C' and (resid 29 through 38 )C29 - 38

+
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://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