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- PDB-7uwo: Structure of beta-catenin in complex with FP05874, a Helicon Poly... -

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Basic information

Entry
Database: PDB / ID: 7uwo
TitleStructure of beta-catenin in complex with FP05874, a Helicon Polypeptide
Components
  • Catenin beta-1
  • Helicon Polypeptide FP05874
KeywordsTRANSCRIPTION / Inhibitor / complex / stapled
Function / homology
Function and homology information


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 ...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 / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / Binding of TCF/LEF:CTNNB1 to target gene promoters / central nervous system vasculogenesis / regulation of centriole-centriole cohesion / RUNX3 regulates WNT signaling / regulation of centromeric sister chromatid cohesion / Regulation of CDH11 function / embryonic axis specification / Specification of the neural plate border / lens morphogenesis in camera-type eye / Scrib-APC-beta-catenin complex / regulation of fibroblast proliferation / beta-catenin-TCF complex / acinar cell differentiation / synaptic vesicle clustering / dorsal root ganglion development / endodermal cell fate commitment / neuron fate determination / proximal/distal pattern formation / Formation of the nephric duct / endothelial tube morphogenesis / positive regulation of fibroblast growth factor receptor signaling pathway / sympathetic ganglion development / dorsal/ventral axis specification / layer formation in cerebral cortex / presynaptic active zone cytoplasmic component / positive regulation of endothelial cell differentiation / fungiform papilla formation / mesenchymal to epithelial transition / hindbrain development / positive regulation of skeletal muscle tissue development / lung epithelial cell differentiation / positive regulation of determination of dorsal identity / fascia adherens / regulation of protein localization to cell surface / hair cell differentiation / ectoderm development / embryonic foregut morphogenesis / cellular response to indole-3-methanol / detection of muscle stretch / positive regulation of odontoblast differentiation / smooth muscle cell differentiation / mesenchymal cell proliferation involved in lung development / positive regulation of myoblast proliferation / alpha-catenin binding / histone methyltransferase binding / regulation of epithelial to mesenchymal transition / regulation of calcium ion import / Germ layer formation at gastrulation / positive regulation of homotypic cell-cell adhesion / negative regulation of oligodendrocyte differentiation / establishment of blood-retinal barrier / flotillin complex / apicolateral plasma membrane / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / cranial skeletal system development / cell-cell adhesion mediated by cadherin / male genitalia development / epithelial cell proliferation involved in prostate gland development / Formation of definitive endoderm / regulation of smooth muscle cell proliferation / catenin complex / embryonic brain development / lung-associated mesenchyme development / oocyte development / beta-catenin destruction complex / establishment of blood-brain barrier / midbrain dopaminergic neuron differentiation / Formation of axial mesoderm / negative regulation of protein sumoylation / Apoptotic cleavage of cell adhesion proteins / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / gastrulation with mouth forming second / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants
Similarity search - Function
Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
N,N'-(1,4-phenylene)diacetamide / Catenin beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsAgarwal, S. / Thomson, T. / Wahl, S. / Ramirez, J. / Hriniak, B. / Verdine, G. / McGee, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: De novo mapping of alpha-helix recognition sites on protein surfaces using unbiased libraries.
Authors: Li, K. / Tokareva, O.S. / Thomson, T.M. / Wahl, S.C.T. / Travaline, T.L. / Ramirez, J.D. / Choudary, S.K. / Agarwal, S. / Walkup 4th, W.G. / Olsen, T.J. / Brennan, M.J. / Verdine, G.L. / McGee, J.H.
History
DepositionMay 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catenin beta-1
B: Helicon Polypeptide FP05874
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1793
Polymers59,9862
Non-polymers1921
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-10 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.128, 85.780, 205.754
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-749-

HOH

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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/peptide Helicon Polypeptide FP05874


Mass: 1847.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.05M MgCl2, 0.1M MES pH6.5, 5% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→53.35 Å / Num. obs: 15896 / % possible obs: 98.55 % / Redundancy: 6.7 % / Biso Wilson estimate: 70.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06713 / Net I/σ(I): 16.64
Reflection shellResolution: 2.75→2.848 Å / Rmerge(I) obs: 0.6669 / Num. unique obs: 1555 / CC1/2: 0.853

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Processing

Software
NameVersionClassification
PHENIX1.20_4444refinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jdh

1jdh


Resolution: 2.75→53.35 Å / SU ML: 0.3965 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.5721
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2534 756 4.76 %
Rwork0.2045 15140 -
obs0.2068 15896 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.43 Å2
Refinement stepCycle: LAST / Resolution: 2.75→53.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3973 0 14 78 4065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414081
X-RAY DIFFRACTIONf_angle_d0.65115538
X-RAY DIFFRACTIONf_chiral_restr0.04669
X-RAY DIFFRACTIONf_plane_restr0.0051708
X-RAY DIFFRACTIONf_dihedral_angle_d3.9418569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.960.32611470.29052948X-RAY DIFFRACTION98.1
2.96-3.260.29771550.24962996X-RAY DIFFRACTION98.62
3.26-3.730.29291310.23953002X-RAY DIFFRACTION98.4
3.73-4.70.23531690.1723020X-RAY DIFFRACTION99.04
4.7-53.350.23071540.18873174X-RAY DIFFRACTION98.61
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)
13.527994508671.08814623681-0.5497044655656.55113812994-1.779078425133.84613202472-0.045126554154-0.155385015317-0.5218613781450.1337620731070.1490543261030.1350832475080.549942825336-0.36994431146-0.08731809566750.417875422791-0.048118599817-0.02009451143590.5012976157150.01550136377250.3750761470424.40352833393-12.1704612675-9.88190733063
21.81723243583-0.06587037223280.1966454506871.19485332152-2.094363252937.19942803237-0.0916961834570.232492730857-0.0446986442935-0.09946442964810.0609772196195-0.004702724513430.368874819426-0.2526656579670.002001004737680.432928036725-0.05017986223720.04234852699130.405863155323-0.03325398968990.47993226147618.362094286723.4443718949-47.7917590374
34.82258551129-2.551408221141.989608629172.339068640370.5418255581135.75448503623-0.1083905310410.05254471180990.2787247528570.1811828829720.5412686207820.222549926498-0.870884639109-1.081733731-0.4288755694020.947748718019-0.006323290617830.1835499370231.28274189735-0.1533617816241.023855084888.0153760111136.3864610988-53.7332194092
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 152 through 391 )AA152 - 3911 - 240
22chain 'A' and (resid 392 through 664 )AA392 - 664241 - 504
33chain 'B' and (resid 2 through 17 )BC2 - 171 - 16

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