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

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Basic information

Entry
Database: PDB / ID: 8eic
TitleCrystal structure of beta-catenin and the MDM2 p53-binding domain in complex with H330, a Helicon Polypeptide
Components
  • Catenin beta-1
  • E3 ubiquitin-protein ligase Mdm2
  • H330
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 / mesenchymal cell proliferation involved in lung development / response to water-immersion restraint stress / 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 / response to ether / 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 / establishment of blood-brain barrier / male genitalia development / negative regulation of oligodendrocyte differentiation / apicolateral plasma membrane / negative regulation of signal transduction by p53 class mediator / fascia adherens / epithelial cell proliferation involved in prostate gland development / 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: 2.62 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: H330
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0904
Polymers71,8983
Non-polymers1921
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-20 kcal/mol
Surface area26920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.110, 71.540, 164.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 H330


Mass: 2659.904 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 4M Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.62→46.36 Å / Num. obs: 20670 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.139 / Net I/σ(I): 14.4
Reflection shellResolution: 2.62→2.74 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2482 / CC1/2: 0.685

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7UWI

7uwi


Resolution: 2.62→43.53 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2694 992 4.81 %
Rwork0.2258 19624 -
obs0.228 20616 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.1 Å2 / Biso mean: 71.399 Å2 / Biso min: 36.37 Å2
Refinement stepCycle: final / Resolution: 2.62→43.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4775 0 14 11 4800
Biso mean--86.83 52.39 -
Num. residues----618
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.62-2.760.33371470.297427662913
2.76-2.930.33641310.270827442875
2.93-3.160.30321480.26627482896
3.16-3.470.30571350.254827832918
3.47-3.980.27991240.225528192943
3.98-5.010.23731520.202228122964
5.01-43.530.24341550.202729523107
Refinement TLS params.Method: refined / Origin x: 0.0373 Å / Origin y: -13.3284 Å / Origin z: 48.4573 Å
111213212223313233
T0.3622 Å20.0011 Å20.0703 Å2-0.2552 Å2-0.0594 Å2--0.3643 Å2
L1.78 °2-0.0284 °21.0405 °2-0.9383 °2-0.3585 °2--1.6982 °2
S-0.0628 Å °-0.0988 Å °0.0519 Å °0.0656 Å °0.1289 Å °0.0325 Å °-0.2358 Å °-0.0375 Å °-0.0606 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA149 - 664
2X-RAY DIFFRACTION1allB25 - 110
3X-RAY DIFFRACTION1allC6 - 101
4X-RAY DIFFRACTION1allS1 - 13

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