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- PDB-8eia: Crystal structure of beta-catenin and the MDM2 p53-binding domain... -

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Basic information

Entry
Database: PDB / ID: 8eia
TitleCrystal structure of beta-catenin and the MDM2 p53-binding domain in complex with H333, a Helicon Polypeptide
Components
  • Catenin beta-1
  • E3 ubiquitin-protein ligase Mdm2
  • H333
KeywordsLIGASE / E3 ligase / complex / stapled peptide
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 / 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 / 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 / cellular response to vitamin B1 / response to formaldehyde / 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 / response to water-immersion restraint stress / 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 / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Germ layer formation at gastrulation / response to ether / establishment of blood-brain barrier / male genitalia development / negative regulation of oligodendrocyte differentiation / negative regulation of signal transduction by p53 class mediator / fascia adherens / epithelial cell proliferation involved in prostate gland development / apicolateral plasma membrane / embryonic brain development / fibroblast activation / Formation of definitive endoderm / atrial septum development / 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 / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / oocyte development / beta-catenin destruction complex / lung-associated mesenchyme development / Formation of axial mesoderm / receptor serine/threonine kinase binding / Trafficking of AMPA receptors
Similarity search - Function
Beta-catenin / E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat ...Beta-catenin / E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Zn-finger in Ran binding protein and others / Zinc finger, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Armadillo/beta-catenin-like repeats / Armadillo / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
N,N'-(1,4-phenylene)diacetamide / Catenin beta-1 / E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsLi, K. / Travaline, T.L. / Swiecicki, J.-M. / Tokareva, O.S. / Thomson, T.M. / Verdine, G.L. / McGee, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2023
Title: Recognition and reprogramming of E3 ubiquitin ligase surfaces by alpha-helical peptides.
Authors: Tokareva, O.S. / Li, K. / Travaline, T.L. / Thomson, T.M. / Swiecicki, J.M. / Moussa, M. / Ramirez, J.D. / Litchman, S. / Verdine, G.L. / McGee, J.H.
History
DepositionSep 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catenin beta-1
B: E3 ubiquitin-protein ligase Mdm2
C: H333
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0544
Polymers71,8623
Non-polymers1921
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-21 kcal/mol
Surface area28250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.810, 96.066, 76.790
Angle α, β, γ (deg.)90.000, 106.620, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 58139.312 Da / Num. of mol.: 1
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 E3 ubiquitin-protein ligase Mdm2 / Double minute 2 protein / Hdm2 / Oncoprotein Mdm2 / RING-type E3 ubiquitin transferase Mdm2 / p53- ...Double minute 2 protein / Hdm2 / Oncoprotein Mdm2 / RING-type E3 ubiquitin transferase Mdm2 / p53-binding protein Mdm2


Mass: 11099.000 Da / Num. of mol.: 1 / Fragment: P53 binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDM2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q00987, RING-type E3 ubiquitin transferase
#3: Protein/peptide H333


Mass: 2623.918 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


Mass: 192.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O2
Has ligand of interestN

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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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Potassium chloride, 0.1 M HEPES pH 7, 15% w/v PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 3.6→48.03 Å / Num. obs: 7517 / % possible obs: 92.31 % / Redundancy: 5.5 % / Biso Wilson estimate: 86.83 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.241 / Net I/σ(I): 5.3
Reflection shellResolution: 3.6→3.94 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.912 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1803 / CC1/2: 0.491 / % possible all: 94.29

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7UWI

7uwi


Resolution: 3.6→47.73 Å / SU ML: 0.6739 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.6938
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3727 1466 10.01 %
Rwork0.3537 13180 -
obs0.3555 7000 92.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.55 Å2
Refinement stepCycle: LAST / Resolution: 3.6→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4713 0 14 0 4727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00264802
X-RAY DIFFRACTIONf_angle_d0.58126509
X-RAY DIFFRACTIONf_chiral_restr0.0365781
X-RAY DIFFRACTIONf_plane_restr0.003823
X-RAY DIFFRACTIONf_dihedral_angle_d12.43531776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.730.38371490.42251346X-RAY DIFFRACTION94.44
3.73-3.880.39311410.37161343X-RAY DIFFRACTION93.51
3.88-4.050.48191570.38981302X-RAY DIFFRACTION93.77
4.05-4.270.4591400.38621288X-RAY DIFFRACTION90.44
4.27-4.530.32721480.38621360X-RAY DIFFRACTION93.55
4.54-4.880.34871410.36661307X-RAY DIFFRACTION92.41
4.89-5.370.42731450.37641311X-RAY DIFFRACTION92.74
5.38-6.150.3981470.41741328X-RAY DIFFRACTION93.47
6.15-7.740.32641510.35891308X-RAY DIFFRACTION92.11
7.75-47.730.31181470.24781287X-RAY DIFFRACTION90.82
Refinement TLS params.Method: refined / Origin x: 7.74981909216 Å / Origin y: 13.7179774078 Å / Origin z: 20.7883535427 Å
111213212223313233
T0.410882221015 Å2-0.18633809336 Å20.0523346245859 Å2-0.648120777016 Å20.0194090104885 Å2--0.615570899768 Å2
L3.72061644069 °2-1.5878044546 °21.31042720874 °2-2.65001436398 °2-1.31109377463 °2--2.2178788014 °2
S0.190815684756 Å °0.0209967152015 Å °0.268491031634 Å °-0.12321762993 Å °-0.0318964778129 Å °0.400188837285 Å °0.0903446317118 Å °-0.26649489975 Å °-0.127092850679 Å °
Refinement TLS groupSelection details: all

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