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5xfl

Crystal structure of the force-sensing device region of alpha N-catenin

Method: X-RAY DIFFRACTION Dmax: 162.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Catenin alpha-2

Mus musculus

UniProt Q61301

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 260–632 Fragment：UNP residues 260-632 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；277 K；100MM HEPES, 20% PEG3350, 200MM POTASSIUM FORMATE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K Resolution 2.45 Å R-free 0.267
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 260–632 Fragment：UNP residues 260-632 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；277 K；100MM HEPES, 20% PEG3350, 200MM POTASSIUM FORMATE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K Resolution 2.45 Å R-free 0.267
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 260–632 Fragment：UNP residues 260-632 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；277 K；100MM HEPES, 20% PEG3350, 200MM POTASSIUM FORMATE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K Resolution 2.45 Å R-free 0.267
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 260–632 Fragment：UNP residues 260-632 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；277 K；100MM HEPES, 20% PEG3350, 200MM POTASSIUM FORMATE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K Resolution 2.45 Å R-free 0.267

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 5XFL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4K1O Crystal structure of the alphaN-catenin actin-binding domain Deposited 2013-04-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 651–905（255 aa） Fragment：C-terminal actin-binding domain
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；0.1M HEPES, pH 7.0, 1.6 M (NH4)2SO4, 0.2 M NaCl,and 0.1M K/Na tartate, vapor diffusion, temperature 277K
Resolution 2.60 Å R-free 0.231
4K1O Crystal structure of the alphaN-catenin actin-binding domain Deposited 2013-04-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 651–905（255 aa） Fragment：C-terminal actin-binding domain
Not recorded SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；0.1M HEPES, pH 7.0, 1.6 M (NH4)2SO4, 0.2 M NaCl,and 0.1M K/Na tartate, vapor diffusion, temperature 277K
Resolution 2.60 Å R-free 0.231
4ONS Structural and thermodynamic characterization of cadherin-beta-catenin-alpha-catenin complex formation Deposited 2014-01-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 18–264（247 aa） Fragment：beta-catenin binding domain, UNP residues 18-264
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；283 K；100mM Tris-Cl, 22% polyethylene glycol monomethryl ether, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.80 Å R-free 0.264
4ONS Structural and thermodynamic characterization of cadherin-beta-catenin-alpha-catenin complex formation Deposited 2014-01-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 18–264（247 aa） Fragment：beta-catenin binding domain, UNP residues 18-264
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；283 K；100mM Tris-Cl, 22% polyethylene glycol monomethryl ether, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.80 Å R-free 0.264
4P9T Structure of the free form of the N-terminal VH1 domain of monomeric alpha-catenin Deposited 2014-04-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 13–261（249 aa） Fragment：UNP residues 13-261
Not recorded IOD IODIDE ION × 5 EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG3350, 0.1 M Bis-Tris propane (pH 6.5), 0.2 M Sodium iodide
Resolution 2.50 Å R-free 0.234
4P9T Structure of the free form of the N-terminal VH1 domain of monomeric alpha-catenin Deposited 2014-04-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 13–261（249 aa） Fragment：UNP residues 13-261
Not recorded IOD IODIDE ION × 5 EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG3350, 0.1 M Bis-Tris propane (pH 6.5), 0.2 M Sodium iodide
Resolution 2.50 Å R-free 0.234
4P9T Structure of the free form of the N-terminal VH1 domain of monomeric alpha-catenin Deposited 2014-04-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 13–261（249 aa） Fragment：UNP residues 13-261
Not recorded IOD IODIDE ION × 5 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG3350, 0.1 M Bis-Tris propane (pH 6.5), 0.2 M Sodium iodide
Resolution 2.50 Å R-free 0.234
4P9T Structure of the free form of the N-terminal VH1 domain of monomeric alpha-catenin Deposited 2014-04-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 13–261（249 aa） Fragment：UNP residues 13-261
Not recorded IOD IODIDE ION × 5 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG3350, 0.1 M Bis-Tris propane (pH 6.5), 0.2 M Sodium iodide
Resolution 2.50 Å R-free 0.234
6DUY Crystal structure of the alpha-N-catenin actin-binding domain H1 mutant Deposited 2018-06-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 664–918（255 aa）
Chain B 664–918（255 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100 mM sodium acetate/acetic acid, pH 4.5, 0.8 M sodium phosphate monobasic, 1.2 M potassium phosphate dibasic
Resolution 2.81 Å R-free 0.255

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

View Construct and Data Evidence
UniProt name CTNA2_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–375； UniProt 260–632 Author chain B； PDBConstruct 3–375； UniProt 260–632 Author chain C； PDBConstruct 3–375； UniProt 260–632 Author chain D； PDBConstruct 3–375； UniProt 260–632

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 5xfl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5xfl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5xfl
Deposition date deposition_date2017-04-10
Structure title titleCrystal structure of the force-sensing device region of alpha N-catenin
Keywords keywordsMECHANOTRANSDUCTION, CYTOSKELETON, 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_guinier46.64 Å
Radius of gyration Rg (electron density) rg_electron47.02 Å
Forward intensity I(0) i0390101000.00
Molecular weight molecular_weight157480.0 kDa
Excluded volume excluded_volume195490 ų
Envelope volume envelope_volume289380 ų
Hydration-shell volume shell_volume55018 ų
Envelope diameter envelope_diameter175.6 Å
Shell Rg shell_rg46.97 Å
Envelope Rg envelope_rg46.18 Å
Shape Rg shape_rg47.02 Å
Total Rg total_rg47.02 Å
Total atoms total_atoms11031
Residues n_residues1425
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 dmax162.8 Å
Rg (real space) rg_real47.03 Å
Rg uncertainty (real space) rg_real_error1.94 Å
I(0) (real space) i0_real3.9010e+08
I(0) uncertainty (real space) i0_real_error8.0340e+06
Rg (reciprocal space) rg_reciprocal46.64 Å
I(0) (reciprocal space) i0_reciprocal389900000.0000
Solution quality estimate total_estimate0.8553
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.1 Å
Skewness Skewness skewness0.468
Kurtosis Kurtosis kurtosis-0.416
Angular range angular_range— – 0.1700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha29280000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.785; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.925; Smooth: 0.836
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5xflA02
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_id5xflB02
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_id5xflC02
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_id5xflD02
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)