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- PDB-4r0z: A conserved phosphorylation switch controls the interaction betwe... -

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Basic information

Entry
Database: PDB / ID: 4r0z
TitleA conserved phosphorylation switch controls the interaction between cadherin and beta-catenin in vitro and in vivo
ComponentsProtein humpback-2
KeywordsCELL ADHESION / armadillo repeat
Function / homology
Function and homology information


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 / RHOH GTPase cycle / Transcriptional Regulation by VENTX / RUNX3 regulates WNT signaling / RHOA GTPase cycle / RHOQ GTPase cycle / Deactivation of the beta-catenin transactivating complex ...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 / RHOH GTPase cycle / Transcriptional Regulation by VENTX / RUNX3 regulates WNT signaling / RHOA 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 / Myogenesis / VEGFR2 mediated vascular permeability / Ca2+ pathway / Neutrophil degranulation / embryonic body morphogenesis / cell migration involved in gastrulation / left/right axis specification / 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 / establishment of mitotic spindle orientation / canonical Wnt signaling pathway / adherens junction / cell-cell adhesion / regulation of protein localization / cell migration / protein phosphatase binding / DNA-binding transcription factor binding / transcription coactivator activity / cadherin binding / protein domain specific binding / protein kinase binding / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / Beta-catenin-like protein hmp-2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.005 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
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein humpback-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1054
Polymers68,9671
Non-polymers1383
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.225, 38.972, 101.128
Angle α, β, γ (deg.)90.000, 116.670, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein humpback-2


Mass: 68966.625 Da / Num. of mol.: 1 / Fragment: UNP residues 53-678
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: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.11 Å3/Da / Density % sol: 41.69 % / Mosaicity: 0.976 °
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.3M sodium formate, 50mM HEPES, pH 7.5, 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: 1.0332 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 24, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 36385 / % possible obs: 93 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Biso Wilson estimate: 29.63 Å2 / Rmerge(I) obs: 0.038 / Χ2: 1.204 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.074.40.22231540.97881.2
2.07-2.154.50.16532641.02483.9
2.15-2.254.50.12533901.0688
2.25-2.374.50.09435191.04591.5
2.37-2.524.40.07737561.05495.9
2.52-2.714.40.06138001.13297.9
2.71-2.994.50.04638461.1598.4
2.99-3.424.60.03638281.36398
3.42-4.314.50.02838671.5797.7
4.31-504.50.02539611.53297.3

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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
Starting model: PDB ID 1I7W

1i7w


Resolution: 2.005→33.674 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 29.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 2783 7.66 %random
Rwork0.1956 ---
obs0.1987 36351 92.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 248.95 Å2 / Biso mean: 41.543 Å2 / Biso min: 10.93 Å2
Refinement stepCycle: LAST / Resolution: 2.005→33.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4250 0 9 130 4389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034370
X-RAY DIFFRACTIONf_angle_d0.7475941
X-RAY DIFFRACTIONf_chiral_restr0.026720
X-RAY DIFFRACTIONf_plane_restr0.004772
X-RAY DIFFRACTIONf_dihedral_angle_d11.6631642
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0046-2.03910.31951070.22951314142173
2.0391-2.07620.28761100.22431489159982
2.0762-2.11610.28071110.2361537164885
2.1161-2.15930.28521080.21741529163783
2.1593-2.20630.28391320.21931535166787
2.2063-2.25760.29861330.20661583171688
2.2576-2.3140.24741370.20061599173689
2.314-2.37660.25931330.21665179893
2.3766-2.44650.22831410.20681702184394
2.4465-2.52540.26381470.21711737188497
2.5254-2.61560.29321570.21371756191397
2.6156-2.72030.26391450.22591774191998
2.7203-2.84410.261550.23441770192598
2.8441-2.99390.33091470.22851797194498
2.9939-3.18140.28121590.22981749190898
3.1814-3.42680.25061500.21771778192898
3.4268-3.77120.24691390.19391791193098
3.7712-4.3160.1571540.15991804195898
4.316-5.4340.18721490.16311817196698
5.434-33.6790.19521690.16131842201196
Refinement TLS params.

S33: 0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0028-0.0015-0.00050.00140.00220.00190.01390.0088-0.0020.0818-0.00370.00610.0136-0.0090.20630.00770.00970.26180.14330.1748-31.5375-31.7119-3.2056
20.00120.0025-0.0021-0.0006-0.0029-0.00090.04280.01010.00540.01530.03630.01610.02320.00680.21450.02340.00060.18590.04910.2192-18.3786-32.76584.4811
30.01790.02270.0124-0.06480.0028-0.00320.0151-0.02760.0119-0.08480.0604-0.0153-0.04070.07710.0424-0.11460.0466-0.04380.121-0.014315.0858-17.088127.0452
40.00450.0027-0.0010.0044-0.00390.00390.0196-0.00730.0079-0.0322-0.00910.00840.01670.01060.1845-0.03270.00850.1441-0.00140.238852.8795-8.572624.4096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 56:109A56 - 109
2X-RAY DIFFRACTION2chain A and resid 110:164A110 - 164
3X-RAY DIFFRACTION3chain A and resid 165:521A165 - 521
4X-RAY DIFFRACTION4chain A and resid 522:612A522 - 612

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