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6dv1

Crystal structure of the alpha-E-catenin actin-binding domain

Method: X-RAY DIFFRACTION Dmax: 89.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Catenin alpha-1

Mus musculus

UniProt P26231

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 652–906 Chain B； UniProt 652–906 Not recorded BR BROMIDE ION × 5 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M potassium bromide, 2.2 M ammonium sulfate, 3% w/v D-galactose Resolution 2.20 Å R-free 0.252

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6DV1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DOV CRYSTAL STRUCTURE OF THE ALPHA-CATENIN DIMERIZATION DOMAIN Deposited 1999-12-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 82–262（181 aa） Fragment：DIMERIZATION DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；295 K；PEG 400, Tris, urea, dithiothreitol, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.00 Å R-free 0.263
1DOV CRYSTAL STRUCTURE OF THE ALPHA-CATENIN DIMERIZATION DOMAIN Deposited 1999-12-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 82–262（181 aa） Fragment：DIMERIZATION DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；295 K；PEG 400, Tris, urea, dithiothreitol, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.00 Å R-free 0.263
1DOW CRYSTAL STRUCTURE OF A CHIMERA OF BETA-CATENIN AND ALPHA-CATENIN Deposited 1999-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 57–261（205 aa） Fragment：DIMERIZATION AND BETA-CATENIN BINDING REGION
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 2000 monomethylether, HEPES, urea, ethanol, Dithiothreitol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Resolution 1.80 Å R-free 0.233
4E17 Alpha-E-catenin is an autoinhibited molecule that co-activates vinculin Deposited 2012-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 321–356（36 aa） Fragment：vinculin binding domain (UNP residues 321-356)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；283 K；20% PEG8000, 100 mM MES, pH 6.8, 3 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.30 Å R-free 0.240
4E18 Alpha-E-catenin is an autoinhibited molecule that co-activates vinculin Deposited 2012-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 302–356（55 aa） Fragment：vinculin binding domain (UNP residues 302-356)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；22% PEG3350, 100 mM bis-tris-propane, pH 8.0, 100 mM sodium nitrate, 3 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.273
4K1N Crystal structure of full-length mouse alphaE-catenin Deposited 2013-04-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–906（906 aa）
Chain B 1–906（906 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.2 M Sodium Citrate, 20% (w/v) PEG-3350, vapor diffusion, temperature 293K
Resolution 6.50 Å R-free 0.247
5Y04 Crystal Structure of the complex between the vinculin D1 domain and alphaE-catenin Deposited 2017-07-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 276–375（100 aa） Fragment：UNP RESIDUES 276-375
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；100MM IMIDAZOLE, 0.5-0.7M POTASSIUM TARTRATE, 0.35M SODIUM FORMATE
Resolution 2.85 Å R-free 0.281
6O3E mouse aE-catenin 82-883 Deposited 2019-02-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 82–883（802 aa）
Chain B 82–883（802 aa）
Mutation：C116S Mutation：C116S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；50 mM Tris, pH 8.5, 60 mM lithium sulfate, 23.5 % PEG 400
Resolution 4.00 Å R-free 0.243
6WVT Structural basis of alphaE-catenin - F-actin catch bond behavior Deposited 2020-05-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain K 671–906（236 aa）
Chain L 671–906（236 aa）
Chain N 671–906（236 aa）
Chain O 671–906（236 aa）
Chain Q 671–906（236 aa）
Chain X 671–906（236 aa）
Not recorded MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.56 Å
9DVA F-actin binding interface of alpha-E-catenin ABD (cadherin-catenin complex) and afadin Deposited 2024-10-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–906（906 aa）
Chain H 1–906（906 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CTNA1_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 9–263； UniProt 652–906 Author chain B； PDBConstruct 9–263； UniProt 652–906

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6dv1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6dv1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6dv1
Deposition date deposition_date2018-06-22
Structure title titleCrystal structure of the alpha-E-catenin actin-binding domain
Keywords keywordsfive-helix bundle, F-actin-binding, mechanosensor, CELL ADHESION; CELL ADHESION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.72 Å
Radius of gyration Rg (electron density) rg_electron23.89 Å
Forward intensity I(0) i033554600.00
Molecular weight molecular_weight42987.0 kDa
Excluded volume excluded_volume53170 ų
Envelope volume envelope_volume66702 ų
Hydration-shell volume shell_volume23704 ų
Envelope diameter envelope_diameter88.4 Å
Shell Rg shell_rg30.54 Å
Envelope Rg envelope_rg24.27 Å
Shape Rg shape_rg23.87 Å
Total Rg total_rg24.73 Å
Total atoms total_atoms2965
Residues n_residues389
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax89.9 Å
Rg (real space) rg_real24.70 Å
Rg uncertainty (real space) rg_real_error0.77 Å
I(0) (real space) i0_real3.3550e+07
I(0) uncertainty (real space) i0_real_error5.7490e+05
Rg (reciprocal space) rg_reciprocal24.71 Å
I(0) (reciprocal space) i0_reciprocal33550000.0000
Solution quality estimate total_estimate0.8499
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.0 Å
Skewness Skewness skewness0.303
Kurtosis Kurtosis kurtosis-0.314
Angular range angular_range— – 0.3200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5966000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.733; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.847; Smooth: 1.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6dv1A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily230 — Alpha-catenin/vinculin-like
Domain ID domain_id6dv1B00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily230 — Alpha-catenin/vinculin-like
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8. Citations (1)

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9. Files and Curves (10)