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- PDB-4r11: A conserved phosphorylation switch controls the interaction betwe... -

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Basic information

Entry
Database: PDB / ID: 4r11
TitleA conserved phosphorylation switch controls the interaction between cadherin and beta-catenin in vitro and in vivo
Components
  • Cadherin-related hmr-1
  • Protein humpback-2
KeywordsCELL ADHESION/PROTEIN BINDING / armadillo repeat / cell adhesion / phosphorylation / CELL ADHESION-PROTEIN BINDING complex
Function / homology
Function and homology information


apical constriction involved in gastrulation / Degradation of beta-catenin by the destruction complex / Beta-catenin phosphorylation cascade / TCF dependent signaling in response to WNT / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / Formation of the cornified envelope / RHOH GTPase cycle / Transcriptional Regulation by VENTX / RUNX3 regulates WNT signaling / RHOA GTPase cycle ...apical constriction involved in gastrulation / Degradation of beta-catenin by the destruction complex / Beta-catenin phosphorylation cascade / TCF dependent signaling in response to WNT / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / Formation of the cornified envelope / RHOH GTPase cycle / Transcriptional Regulation by VENTX / RUNX3 regulates WNT signaling / RHOA GTPase cycle / RHOB GTPase cycle / RHOQ GTPase cycle / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex / Apoptotic cleavage of cell adhesion proteins / VEGFR2 mediated vascular permeability / Ca2+ pathway / Neutrophil degranulation / embryonic body morphogenesis / distal dendrite / cell migration involved in gastrulation / left/right axis specification / delta-catenin binding / negative regulation of cell division / cell-cell adhesion mediated by cadherin / alpha-catenin binding / catenin complex / embryo development ending in birth or egg hatching / cortical actin cytoskeleton organization / molecular function inhibitor activity / homophilic cell adhesion via plasma membrane adhesion molecules / establishment of mitotic spindle orientation / canonical Wnt signaling pathway / gastrulation / adherens junction / beta-catenin binding / cell-cell adhesion / regulation of protein localization / cell migration / nervous system development / protein phosphatase binding / DNA-binding transcription factor binding / transcription coactivator activity / cadherin binding / protein domain specific binding / calcium ion binding / protein kinase binding / positive regulation of transcription by RNA polymerase II / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Beta-catenin / Laminin G domain / Laminin G domain profile. / Cadherin / Laminin G domain / Laminin G domain / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain ...Beta-catenin / Laminin G domain / Laminin G domain profile. / Cadherin / Laminin G domain / Laminin G domain / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / EGF-type aspartate/asparagine hydroxylation site / Aspartic acid and asparagine hydroxylation site. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Armadillo-like helical / Alpha Horseshoe / Concanavalin A-like lectin/glucanase domain superfamily / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Beta-catenin-like protein hmp-2 / Cadherin-related hmr-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.789 Å
AuthorsChoi, H.-J. / Loveless, T. / Lynch, A. / Bang, I. / Hardin, J. / Weis, W.I.
CitationJournal: Dev.Cell / Year: 2015
Title: A Conserved Phosphorylation Switch Controls the Interaction between Cadherin and beta-Catenin In Vitro and In Vivo
Authors: Choi, H.J. / Loveless, T. / Lynch, A.M. / Bang, I. / Hardin, J. / Weis, W.I.
History
DepositionAug 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein humpback-2
B: Cadherin-related hmr-1
C: Protein humpback-2
D: Cadherin-related hmr-1
E: Protein humpback-2
F: Cadherin-related hmr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,58315
Polymers215,4416
Non-polymers1,1429
Water93752
1
A: Protein humpback-2
B: Cadherin-related hmr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3216
Polymers71,8142
Non-polymers5084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-12 kcal/mol
Surface area24850 Å2
MethodPISA
2
C: Protein humpback-2
D: Cadherin-related hmr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3216
Polymers71,8142
Non-polymers5084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-12 kcal/mol
Surface area24520 Å2
MethodPISA
3
E: Protein humpback-2
F: Cadherin-related hmr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9413
Polymers71,8142
Non-polymers1271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-20 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.057, 157.716, 84.824
Angle α, β, γ (deg.)90.00, 94.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein humpback-2


Mass: 62334.555 Da / Num. of mol.: 3 / Fragment: armadillo domain, UNP residues 53-621
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: hmp-2, K05C4.6 / Production host: Escherichia coli (E. coli) / References: UniProt: O44326
#2: Protein Cadherin-related hmr-1 / Protein Hammerhead


Mass: 9479.077 Da / Num. of mol.: 3 / Fragment: cytoplasmic domain, UNP residues 2841-2920
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: hmr-1, W02B9.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q967F4
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 17% PEG 3350, 0.1M Bis-Tris-Propane, 0.2M sodium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 6, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.789→50 Å / Num. obs: 54788 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 65.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.789-2.93.40.655195.9
2.9-3.023.60.507199.4
3.02-3.153.70.38199.5
3.15-3.323.70.268199.6
3.32-3.533.70.174199.6
3.53-3.83.70.1199.8
3.8-4.183.70.059199.9
4.18-4.793.70.043199.9
4.79-6.033.70.045199.9
6.03-503.70.032199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.789→44.686 Å / SU ML: 0.39 / σ(F): 1.36 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 4261 7.78 %
Rwork0.199 --
obs0.2029 54763 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.5015 Å2
Refinement stepCycle: LAST / Resolution: 2.789→44.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13059 0 9 52 13120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313271
X-RAY DIFFRACTIONf_angle_d0.7418037
X-RAY DIFFRACTIONf_dihedral_angle_d12.2294984
X-RAY DIFFRACTIONf_chiral_restr0.0242176
X-RAY DIFFRACTIONf_plane_restr0.0042336
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.789-2.82070.38961140.3055130477
2.8207-2.85390.35241300.2837160396
2.8539-2.88870.33761540.2647167997
2.8887-2.92520.33731370.2649169699
2.9252-2.96370.31841370.25431670100
2.9637-3.00430.31611380.2449167999
3.0043-3.04720.30771520.2603172799
3.0472-3.09270.33711390.24931667100
3.0927-3.1410.31041240.25471744100
3.141-3.19250.29651420.25541675100
3.1925-3.24750.32571420.2474165899
3.2475-3.30650.31491330.24791722100
3.3065-3.37010.31141500.2331709100
3.3701-3.43890.31391450.23811680100
3.4389-3.51360.2651500.22771711100
3.5136-3.59530.25121320.22431679100
3.5953-3.68520.26781490.21461728100
3.6852-3.78480.30321290.21677100
3.7848-3.89610.25821460.19091725100
3.8961-4.02180.21621480.17451682100
4.0218-4.16540.20681840.16281673100
4.1654-4.33210.20131400.16831681100
4.3321-4.5290.21691540.17121714100
4.529-4.76760.2271550.16541695100
4.7676-5.06590.23891380.17341709100
5.0659-5.45640.28681340.18941729100
5.4564-6.00430.24771290.22291727100
6.0043-6.87050.24231520.19591717100
6.8705-8.64580.19121540.16041708100
8.6458-44.69190.18211300.1709173498
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)
10.18180.0765-0.0939-0.03490.14651.32230.06430.00140.08360.01580.0676-0.02750.1911-0.1814-00.5112-0.105-0.00450.37250.02580.188214.454928.33283.5753
20.261-0.0302-0.222-0.0128-0.07250.0672-0.0195-0.1842-0.0259-0.0368-0.06910.00960.0439-0.029300.9807-0.1443-0.14070.63440.0680.445620.937130.302520.272
31.2274-0.205-0.06940.17530.14170.01950.0640.16090.25190.0067-0.0421-0.00450.0717-0.0001-00.20990.01510.02630.26940.07160.39719.155865.0901-7.8454
40.09360.110.1964-0.10710.07530.1293-0.0554-0.05420.1303-0.25090.03450.31320.05740.0719-00.4304-0.01840.13350.5637-0.05150.83272.039765.71620.5235
50.5725-0.08190.03190.5376-0.14840.68590.0726-0.0871-0.1176-0.24590.02910.0788-0.1568-0.21400.20170.0064-0.06820.27730.02420.297355.156920.985-2.5872
60.1684-0.2492-0.17720.3696-0.0690.08230.0453-0.0951-0.0980.0273-0.18790.24050.01250.1994-00.547-0.0448-0.12220.69730.03920.718160.522322.5225-0.6044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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