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- PDB-1l7c: alpha-catenin fragment, residues 385-651 -

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Basic information

Entry
Database: PDB / ID: 1l7c
Titlealpha-catenin fragment, residues 385-651
ComponentsAlpha E-catenin
KeywordsCELL ADHESION / four-helix bundle
Function / homology
Function and homology information


negative regulation of integrin-mediated signaling pathway / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / VEGFR2 mediated vascular permeability / Adherens junctions interactions / Regulation of CDH11 function / RHO GTPases activate IQGAPs / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens ...negative regulation of integrin-mediated signaling pathway / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / VEGFR2 mediated vascular permeability / Adherens junctions interactions / Regulation of CDH11 function / RHO GTPases activate IQGAPs / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens / gap junction assembly / cellular response to indole-3-methanol / flotillin complex / vinculin binding / Myogenesis / catenin complex / apical junction assembly / negative regulation of cell motility / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smoothened signaling pathway / Adherens junctions interactions / negative regulation of protein localization to nucleus / axon regeneration / negative regulation of neuroblast proliferation / smoothened signaling pathway / Myogenesis / establishment or maintenance of cell polarity / odontogenesis of dentin-containing tooth / intercalated disc / neuroblast proliferation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / RHO GTPases activate IQGAPs / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / acrosomal vesicle / VEGFR2 mediated vascular permeability / integrin-mediated signaling pathway / adherens junction / cell motility / cell-cell adhesion / beta-catenin binding / response to estrogen / male gonad development / actin filament binding / cell-cell junction / cell junction / intracellular protein localization / cell migration / lamellipodium / actin cytoskeleton / regulation of cell population proliferation / cell adhesion / cadherin binding / focal adhesion / intracellular membrane-bounded organelle / apoptotic process / negative regulation of apoptotic process / structural molecule activity / Golgi apparatus / RNA binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Alpha-catenin / Alpha-catenin/vinculin-like / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Catenin alpha-1 / Catenin alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsPokutta, S. / Drees, F. / Takai, Y. / Nelson, W.J. / Weis, W.I.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Biochemical and structural definition of the l-afadin- and actin-binding sites of alpha-catenin.
Authors: Pokutta, S. / Drees, F. / Takai, Y. / Nelson, W.J. / Weis, W.I.
History
DepositionMar 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Alpha E-catenin
B: Alpha E-catenin
C: Alpha E-catenin


Theoretical massNumber of molelcules
Total (without water)90,6213
Polymers90,6213
Non-polymers00
Water1,62190
1
A: Alpha E-catenin


Theoretical massNumber of molelcules
Total (without water)30,2071
Polymers30,2071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha E-catenin


Theoretical massNumber of molelcules
Total (without water)30,2071
Polymers30,2071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha E-catenin


Theoretical massNumber of molelcules
Total (without water)30,2071
Polymers30,2071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Alpha E-catenin
C: Alpha E-catenin


Theoretical massNumber of molelcules
Total (without water)60,4142
Polymers60,4142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-11 kcal/mol
Surface area24670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.780, 105.290, 123.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha E-catenin / Alpha-1 catenin / Cadherin-associated protein


Mass: 30206.965 Da / Num. of mol.: 3 / Fragment: Residues 385-651
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P35221, UniProt: P26231*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: sodium acetate, dithiothreitol, urea, sodium/potassium tartrate, isopropanol, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
180 mg/mlprotein1drop
2700 mMsodium acetate1reservoirpH4.0
310 mMdithiothreitol1reservoir
41.05 Murea1reservoir
5200 mMsodium potassium tartrate1reservoir
63 %isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.9252, 0.9795, 0.9799, 1.0688
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 24, 1999 / Details: double flat monochromator + mirror
RadiationMonochromator: Null / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.92521
20.97951
30.97991
41.06881
ReflectionResolution: 2.5→30 Å / Num. all: 56243 / Num. obs: 54918 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 19.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.237 / Num. unique all: 2734 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.248

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2114134.46 / Data cutoff high rms absF: 2114134.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 5428 9.9 %RANDOM
Rwork0.238 ---
obs0.238 54892 97.2 %-
all-56243 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.5627 Å2 / ksol: 0.339732 e/Å3
Displacement parametersBiso mean: 59.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.06 Å20 Å20 Å2
2---5.08 Å20 Å2
3---0.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5454 0 0 90 5544
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d16.5
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 855 10 %
Rwork0.286 7690 -
obs--91.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor obs: 0.238 / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
LS refinement shell
*PLUS
Rfactor Rfree: 0.342 / Rfactor Rwork: 0.286 / Rfactor obs: 0.286

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