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- PDB-4ons: Structural and thermodynamic characterization of cadherin-beta-ca... -

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Basic information

Entry
Database: PDB / ID: 4ons
TitleStructural and thermodynamic characterization of cadherin-beta-catenin-alpha-catenin complex formation
Components
  • Catenin alpha-2CTNNA2
  • Catenin beta-1
KeywordsCELL ADHESION / four helix bundles
Function / homology
Function and homology information


radial glia guided migration of Purkinje cell / lung cell differentiation / epicardium-derived cardiac vascular smooth muscle cell differentiation / mesenchyme morphogenesis / RUNX3 regulates WNT signaling / Regulation of CDH11 function / cardiac vascular smooth muscle cell differentiation / extrinsic component of postsynaptic membrane / Beta-catenin phosphorylation cascade / regulation of synapse structural plasticity ...radial glia guided migration of Purkinje cell / lung cell differentiation / epicardium-derived cardiac vascular smooth muscle cell differentiation / mesenchyme morphogenesis / RUNX3 regulates WNT signaling / Regulation of CDH11 function / cardiac vascular smooth muscle cell differentiation / extrinsic component of postsynaptic membrane / Beta-catenin phosphorylation cascade / regulation of synapse structural plasticity / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Apoptotic cleavage of cell adhesion proteins / hair cycle process / positive regulation of epithelial cell differentiation / TCF dependent signaling in response to WNT / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / trachea morphogenesis / mesenchyme development / endoderm formation / Formation of the beta-catenin:TCF transactivating complex / VEGFR2 mediated vascular permeability / 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 / Deactivation of the beta-catenin transactivating complex / 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 / extrinsic component of presynaptic membrane / Ca2+ pathway / central nervous system vasculogenesis / regulation of epithelial cell differentiation / Schwann cell proliferation / animal organ development / regulation of centriole-centriole cohesion / glandular epithelial cell differentiation / Degradation of beta-catenin by the destruction complex / modification of postsynaptic actin cytoskeleton / RHO GTPases activate IQGAPs / regulation of centromeric sister chromatid cohesion / Adherens junctions interactions / embryonic axis specification / endodermal cell fate commitment / ventricular compact myocardium morphogenesis / morphogenesis of embryonic epithelium / positive regulation of fibroblast growth factor receptor signaling pathway / Scrib-APC-beta-catenin complex / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / dorsal root ganglion development / negative regulation of Arp2/3 complex-mediated actin nucleation / synaptic vesicle clustering / acinar cell differentiation / regulation of neuron migration / 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 / delta-catenin binding / 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 / regulation of osteoclast differentiation / cranial skeletal system development / endothelial tube morphogenesis / regulation of protein localization to cell surface / cellular response to indole-3-methanol / mesenchymal cell proliferation involved in lung development / presynaptic active zone cytoplasmic component / smooth muscle cell differentiation / histone methyltransferase binding / cell projection membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2780 / Alpha-catenin / Alpha-catenin/vinculin-like / Beta-catenin / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Armadillo/plakoglobin ARM repeat profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2780 / Alpha-catenin / Alpha-catenin/vinculin-like / Beta-catenin / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helix non-globular / Special / Armadillo-like helical / Armadillo-type fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Catenin beta-1 / Catenin alpha-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsPokutta, S. / Choi, H.-J. / Ahlsen, G. / Hansen, S.D. / Weis, W.I.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural and Thermodynamic Characterization of Cadherin beta-Catenin alpha-Catenin Complex Formation.
Authors: Pokutta, S. / Choi, H.J. / Ahlsen, G. / Hansen, S.D. / Weis, W.I.
History
DepositionJan 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2May 28, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catenin alpha-2
B: Catenin beta-1
C: Catenin alpha-2
D: Catenin beta-1


Theoretical massNumber of molelcules
Total (without water)74,5294
Polymers74,5294
Non-polymers00
Water39622
1
A: Catenin alpha-2
B: Catenin beta-1


Theoretical massNumber of molelcules
Total (without water)37,2642
Polymers37,2642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-32 kcal/mol
Surface area14900 Å2
MethodPISA
2
C: Catenin alpha-2
D: Catenin beta-1


Theoretical massNumber of molelcules
Total (without water)37,2642
Polymers37,2642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-34 kcal/mol
Surface area14620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.125, 96.125, 65.517
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Catenin alpha-2 / CTNNA2 / Alpha N-catenin


Mass: 27351.385 Da / Num. of mol.: 2 / Fragment: beta-catenin binding domain, UNP residues 18-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctnna2, Catna2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q61301
#2: Protein Catenin beta-1 / / Beta-catenin


Mass: 9912.957 Da / Num. of mol.: 2 / Fragment: alpha-catenin binding domain, UNP residues 78-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctnnb1, Catnb / Production host: Escherichia coli (E. coli) / References: UniProt: Q02248
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 100mM Tris-Cl, 22% polyethylene glycol monomethryl ether, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2011
RadiationMonochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.794→38.753 Å / Num. all: 16165 / Num. obs: 16165 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 60.42 Å2 / Rsym value: 0.068 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.79-2.953.30.4960.30.496193.1
2.95-3.123.20.272.50.27196.5
3.12-3.343.50.1913.50.191199.2
3.34-3.613.30.1255.20.125198.7
3.61-3.952.90.160.1193.3
3.95-4.423.30.05810.50.058198.4
4.42-5.13.10.048130.048195.1
5.1-6.253.30.04513.10.045197.9
6.25-8.843.30.03116.50.031194.1
8.84-38.7533.30.02817.60.028194.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→38.753 Å / SU ML: 0.45 / σ(F): 1.98 / Phase error: 29.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 1146 7.11 %
Rwork0.2033 --
obs0.2075 16123 96.67 %
all-17269 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.22 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 0 22 4318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034335
X-RAY DIFFRACTIONf_angle_d0.5765829
X-RAY DIFFRACTIONf_dihedral_angle_d11.5881655
X-RAY DIFFRACTIONf_chiral_restr0.021686
X-RAY DIFFRACTIONf_plane_restr0.002759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-2.92760.35321530.28591873X-RAY DIFFRACTION96
2.9276-3.08190.3561320.25161875X-RAY DIFFRACTION96
3.0819-3.27490.29291630.24511873X-RAY DIFFRACTION98
3.2749-3.52760.30541600.21861936X-RAY DIFFRACTION99
3.5276-3.88230.26591240.19861811X-RAY DIFFRACTION93
3.8823-4.44330.23571650.17571854X-RAY DIFFRACTION98
4.4433-5.59540.25281210.191905X-RAY DIFFRACTION96
5.5954-38.75680.22161280.18851850X-RAY DIFFRACTION96
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)
15.5589-1.53390.12444.7523-0.19473.5612-0.0658-0.13530.23340.40240.2419-0.1090.17690.4206-0.09180.2834-0.1411-0.00350.5262-0.09740.419316.4683-28.622323.8499
22.7116-0.699-0.37251.7536-0.34751.85030.1343-0.1947-0.3302-0.0950.1380.12840.9759-0.5111-0.07570.2745-0.2033-0.0580.49310.04060.28125.0813-38.262820.3278
33.0656-2.4284-3.48541.87572.62813.6952-0.2723-0.1469-0.85840.38190.2377-0.17980.35980.34210.08810.36730.09710.15350.646-0.11730.73634.8131-44.7665-3.6731
43.3623-1.1754-1.68211.145-0.18591.54820.58580.57570.52-0.1326-0.3531-0.2242-0.1668-0.272-0.18620.41910.04250.09870.8552-0.11820.649740.2691-39.0101-8.2952
56.288-0.0038-0.73022.84960.16963.60790.0592-0.39370.78830.02840.3975-0.5537-0.88350.4216-0.22740.3864-0.06770.12340.3809-0.10830.4620.1037-26.2213.0565
62.61770.5564-1.55470.7887-0.53882.4212-0.07230.0690.2106-0.11890.33060.07520.1352-0.3435-0.20230.2791-0.0403-0.05350.54340.13170.30488.6884-30.994710.5513
73.50820.70280.87624.4042-1.06984.5984-0.19030.41740.3381-0.63580.3913-0.355-0.1633-0.8982-0.04250.454-0.10480.11650.51130.01230.296917.768-29.1166-29.0231
81.9875-0.7381-0.05032.40530.12722.88410.0579-0.1384-0.1398-0.09050.16140.24120.9852-0.6209-0.08830.5247-0.1236-0.02950.39050.0160.300513.0267-43.3444-25.3396
93.8817-2.6972-4.58641.82773.17045.3498-0.0896-0.269-0.04330.0284-0.36960.8347-0.0704-0.72510.21110.58310.17290.15870.8898-0.01730.6362-3.2139-17.4253-1.6727
104.2024-0.3378-1.3282.16110.36012.75030.4322-1.02560.01430.0786-0.3344-0.2879-0.1449-0.4098-0.04851.18220.0840.20860.9392-0.15161.12642.1049-17.79456.4781
11-0.0184-0.0547-0.0344-0.037-0.052-0.0338-0.2734-0.4470.2280.1632-0.24720.2357-0.4818-0.60090.05061.8422-0.00860.59791.1727-0.38761.56750.0501-6.66919.828
120.2650.0403-0.5939-0.0049-0.11791.1152-0.23920.0072-0.02010.1382-0.1955-0.3339-0.22890.1348-0.00570.990.00360.34410.69340.12711.3843-0.7373-4.61290.5213
135.6536-1.45480.08745.20930.22783.4229-0.2813-0.12450.93210.37960.6684-1.2452-0.83770.8434-0.1350.3954-0.11080.0050.3991-0.18520.514320.2677-24.6466-16.7155
141.7243-0.5048-1.17383.12241.23933.59960.0513-0.06480.2046-0.01220.2002-0.16820.32550.4213-0.17970.41440.0476-0.14280.3325-0.01730.325618.6961-37.64-15.9897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 18:39
2X-RAY DIFFRACTION2chain A and resid 52:147
3X-RAY DIFFRACTION3chain A and resid 148:166
4X-RAY DIFFRACTION4chain A and resid 168:260
5X-RAY DIFFRACTION5chain B and resid 83:103
6X-RAY DIFFRACTION6chain B and resid 109:143
7X-RAY DIFFRACTION7chain C and resid 19:38
8X-RAY DIFFRACTION8chain C and resid 53:147
9X-RAY DIFFRACTION9chain C and resid 148:165
10X-RAY DIFFRACTION10chain C and resid 168:195
11X-RAY DIFFRACTION11chain C and resid 207:228
12X-RAY DIFFRACTION12chain C and resid 237:258
13X-RAY DIFFRACTION13chain D and resid 84:108
14X-RAY DIFFRACTION14chain D and resid 109:144

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