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- PDB-3l6y: Crystal structure of p120 catenin in complex with E-cadherin -

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Basic information

Entry
Database: PDB / ID: 3l6y
TitleCrystal structure of p120 catenin in complex with E-cadherin
Components
  • Catenin delta-1
  • E-cadherinCadherin-1
KeywordsCELL ADHESION / p120 / catenin / cadherin / E-cadherin / armadillo / ARM / JMD / complex / cell-cell adhesion / ARVCF / delta-catenin / p0071 / Dp120 / JAC-1 / Cell membrane / Membrane / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Wnt signaling pathway
Function / homology
Function and homology information


CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / response to Gram-positive bacterium / Regulation of CDH11 function / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / pituitary gland development / gamma-catenin binding / zonula adherens / cell-cell adhesion mediated by cadherin / negative regulation of axon extension ...CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / response to Gram-positive bacterium / Regulation of CDH11 function / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / pituitary gland development / gamma-catenin binding / zonula adherens / cell-cell adhesion mediated by cadherin / negative regulation of axon extension / cellular response to indole-3-methanol / presynaptic active zone cytoplasmic component / flotillin complex / Formation of definitive endoderm / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Adherens junctions interactions / catenin complex / Apoptotic cleavage of cell adhesion proteins / GTPase activating protein binding / cell-cell junction assembly / adherens junction organization / ankyrin binding / apical junction complex / negative regulation of cell-cell adhesion / cellular response to lithium ion / regulation of postsynaptic membrane neurotransmitter receptor levels / homophilic cell adhesion via plasma membrane adhesion molecules / lateral plasma membrane / RHO GTPases activate IQGAPs / postsynaptic density, intracellular component / Integrin cell surface interactions / cell adhesion molecule binding / synapse assembly / InlA-mediated entry of Listeria monocytogenes into host cells / protein sequestering activity / Degradation of the extracellular matrix / hippocampal mossy fiber to CA3 synapse / negative regulation of cell migration / protein tyrosine kinase binding / VEGFR2 mediated vascular permeability / protein localization to plasma membrane / adherens junction / Schaffer collateral - CA1 synapse / trans-Golgi network / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / cytoplasmic side of plasma membrane / response to toxic substance / beta-catenin binding / Wnt signaling pathway / cell-cell adhesion / positive regulation of protein import into nucleus / neuron projection development / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / actin cytoskeleton / cell junction / lamellipodium / midbody / growth cone / postsynapse / regulation of gene expression / dendritic spine / protein stabilization / endosome / response to xenobiotic stimulus / cadherin binding / signaling receptor binding / glutamatergic synapse / calcium ion binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / cell surface / extracellular exosome / extracellular region / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Plakophilin/Delta catenin / Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherin / Cadherin conserved site / Cadherin domain signature. ...Plakophilin/Delta catenin / Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherin / 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 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Catenin delta-1 / Cadherin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsIshiyama, N. / Lee, S.-H. / Liu, S. / Li, G.-Y. / Smith, M.J. / Reichardt, L.F. / Ikura, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: Dynamic and static interactions between p120 catenin and E-cadherin regulate the stability of cell-cell adhesion.
Authors: Ishiyama, N. / Lee, S.H. / Liu, S. / Li, G.Y. / Smith, M.J. / Reichardt, L.F. / Ikura, M.
History
DepositionDec 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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 delta-1
B: E-cadherin
C: Catenin delta-1
D: E-cadherin
E: Catenin delta-1
F: E-cadherin


Theoretical massNumber of molelcules
Total (without water)202,1106
Polymers202,1106
Non-polymers00
Water95553
1
A: Catenin delta-1
B: E-cadherin


Theoretical massNumber of molelcules
Total (without water)67,3702
Polymers67,3702
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-9 kcal/mol
Surface area16400 Å2
MethodPISA
2
C: Catenin delta-1
D: E-cadherin


Theoretical massNumber of molelcules
Total (without water)67,3702
Polymers67,3702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-9 kcal/mol
Surface area17380 Å2
MethodPISA
3
E: Catenin delta-1
F: E-cadherin


Theoretical massNumber of molelcules
Total (without water)67,3702
Polymers67,3702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-9 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.177, 106.177, 173.207
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
12B
22D
32F

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROALAALAAA359 - 78141 - 432
21PROPROALAALACC359 - 78141 - 432
31PROPROALAALAEE359 - 78141 - 432
12ASPASPHISHISBB758 - 7751 - 18
22ASPASPHISHISDD758 - 7751 - 18
32ASPASPHISHISFF758 - 7751 - 18

NCS ensembles :
ID
1
2

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Components

#1: Protein Catenin delta-1 / p120 catenin / p120(ctn) / Cadherin-associated Src substrate / CAS / p120(cas)


Mass: 65348.980 Da / Num. of mol.: 3 / Fragment: p120 catenin isoform 4A / Mutation: deletion mutant (residues 613-643)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNND1, KIAA0384 / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O60716
#2: Protein/peptide E-cadherin / Cadherin-1


Mass: 2020.949 Da / Num. of mol.: 3 / Fragment: E-cadherin juxtamembrane domain core region / Source method: obtained synthetically / References: UniProt: P12830*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS ENTRY MATCHES THE SEQUENCE OF ISOFORM 1A WITH UNIPROT IDENTIFIER O60716-5. ...THE SEQUENCE OF THIS ENTRY MATCHES THE SEQUENCE OF ISOFORM 1A WITH UNIPROT IDENTIFIER O60716-5. RESIDUES 626-631 (EXON C) OF O60716 ARE NOT PART OF ISOFORM 1A.

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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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M HEPES, 8% (w/v) PEG-8000, pH 7.4, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 43627 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rsym value: 0.063 / Χ2: 1.078 / Net I/σ(I): 11.1
Reflection shellResolution: 3→3.05 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 5.12 / Num. unique all: 2210 / Rsym value: 0.331 / Χ2: 0.95 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.72
Highest resolutionLowest resolution
Rotation3 Å34.75 Å
Translation3 Å34.75 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-3000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3L6X

3l6x


Resolution: 3→35 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.264 / WRfactor Rwork: 0.232 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.799 / SU B: 30.114 / SU ML: 0.259 / SU R Cruickshank DPI: 0.988 / SU Rfree: 0.38 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.986 / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2177 5 %RANDOM
Rwork0.232 ---
obs0.233 43284 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.59 Å2 / Biso mean: 55.381 Å2 / Biso min: 26.62 Å2
Baniso -1Baniso -2Baniso -3
1-4.23 Å22.11 Å20 Å2
2--4.23 Å20 Å2
3----6.34 Å2
Refinement stepCycle: LAST / Resolution: 3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9046 0 0 53 9099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0219180
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.96512445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.97351165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6424.393412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.174151564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8741570
X-RAY DIFFRACTIONr_chiral_restr0.090.21458
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216850
X-RAY DIFFRACTIONr_mcbond_it0.4231.55877
X-RAY DIFFRACTIONr_mcangle_it0.84529382
X-RAY DIFFRACTIONr_scbond_it1.38833303
X-RAY DIFFRACTIONr_scangle_it2.4894.53063
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1420TIGHT POSITIONAL0.040.05
12C1420TIGHT POSITIONAL0.040.05
13E1420TIGHT POSITIONAL0.050.05
11A1269LOOSE POSITIONAL0.055
12C1269LOOSE POSITIONAL0.055
13E1269LOOSE POSITIONAL0.075
11A1420TIGHT THERMAL0.070.5
12C1420TIGHT THERMAL0.080.5
13E1420TIGHT THERMAL0.090.5
11A1269LOOSE THERMAL0.0910
12C1269LOOSE THERMAL0.110
13E1269LOOSE THERMAL0.110
21B72TIGHT POSITIONAL0.040.05
22D72TIGHT POSITIONAL0.030.05
23F72TIGHT POSITIONAL0.040.05
21B69LOOSE POSITIONAL0.045
22D69LOOSE POSITIONAL0.045
23F69LOOSE POSITIONAL0.055
21B72TIGHT THERMAL0.070.5
22D72TIGHT THERMAL0.060.5
23F72TIGHT THERMAL0.070.5
21B69LOOSE THERMAL0.0710
22D69LOOSE THERMAL0.0810
23F69LOOSE THERMAL0.0810
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 142 -
Rwork0.322 3075 -
all-3217 -
obs--99.17 %
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)
12.66380.4121.68562.78392.08165.3638-0.011-0.31660.26820.06110.2341-0.304-0.38930.3361-0.2231-0.0397-0.06970.002-0.1215-0.0721-0.038117.338-10.46333.241
24.23771.5241.44444.996-2.02527.6399-0.08630.46690.1402-0.37670.13040.1078-0.2550.0983-0.0442-0.0491-0.0383-0.0415-0.23180.0578-0.15095.056-13.98511.482
35.33171.24710.4094.9811-0.68116.86-0.09360.80730.4866-0.41210.06670.0372-0.57710.28510.0270.212-0.0114-0.03710.05270.1971-0.02071.927-8.089-1.772
44.6143-0.1775-3.2993.97291.07672.5860.04691.2660.3129-0.530.3029-0.1291-0.5972-0.1388-0.34970.7897-0.17590.01850.81390.42570.47547.959-1.329-13.886
51.9749-0.07260.29092.6934-2.18996.71370.114-0.3444-0.1320.1272-0.1071-0.14040.03290.3697-0.0069-0.4044-0.1126-0.0138-0.1340.0076-0.111935.819-41.46423.958
63.2396-0.0301-3.11615.1501-1.18428.4931-0.01440.08610.2024-0.40130.0342-0.0566-0.3429-0.2132-0.0199-0.1476-0.14670.1069-0.28280.0395-0.135138.108-28.2422.125
74.2802-0.0885-0.60526.1647-0.3938.3958-0.17690.1774-0.1695-0.79630.1528-0.27090.2250.12350.02420.0162-0.20750.1728-0.17330.0044-0.099844.697-28.273-11.42
82.8879-0.52450.40965.37050.01260.05950.14540.5214-0.1524-1.1952-0.0410.24660.91530.2441-0.10440.7716-0.10540.240.3449-0.10740.395248.394-37.308-23.327
92.2132-0.385-2.14642.55051.25565.339-0.0021-0.19640.08130.18960.01570.14590.0679-0.0286-0.0137-0.3722-0.0854-0.008-0.30640.0266-0.20323.71-41.21528.959
105.9277-0.3513-0.49533.50391.82599.0255-0.11360.1471-0.0627-0.1756-0.0175-0.13250.01830.14460.1311-0.3309-0.0094-0.053-0.3135-0.1015-0.241912.153-52.2196.96
114.9028-0.33590.17154.4331.53418.19030.20890.3835-0.2555-0.5082-0.39860.3811-0.1219-0.5290.1897-0.1573-0.0162-0.1159-0.2711-0.083-0.17227.321-56.802-6.292
126.42620.2708-0.93648.6584-0.15741.38650.19140.76950.2775-0.8506-0.24320.4902-0.3667-1.23690.05180.39230.1686-0.28080.4466-0.08760.2389-2.316-53.039-18.482
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A359 - 512
2X-RAY DIFFRACTION1B758 - 775
3X-RAY DIFFRACTION2A520 - 599
4X-RAY DIFFRACTION3A645 - 733
5X-RAY DIFFRACTION4A734 - 781
6X-RAY DIFFRACTION5C359 - 511
7X-RAY DIFFRACTION5D758 - 775
8X-RAY DIFFRACTION6C519 - 599
9X-RAY DIFFRACTION7C645 - 733
10X-RAY DIFFRACTION8C734 - 781
11X-RAY DIFFRACTION9E359 - 511
12X-RAY DIFFRACTION9F758 - 775
13X-RAY DIFFRACTION10E518 - 600
14X-RAY DIFFRACTION11E645 - 733
15X-RAY DIFFRACTION12E734 - 782

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