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4p9t

Structure of the free form of the N-terminal VH1 domain of monomeric alpha-catenin

Method: X-RAY DIFFRACTION Dmax: 126.8 Å Quality: REASONABLE
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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 C； UniProt 13–261 Fragment：UNP residues 13-261 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 13–261 Fragment：UNP residues 13-261 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 13–261 Fragment：UNP residues 13-261 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
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 13–261 Fragment：UNP residues 13-261 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

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 4P9T 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 ligand/ion 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 ligand/ion 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
5XFL Crystal structure of the force-sensing device region of alpha N-catenin Deposited 2017-04-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 260–632（373 aa） Fragment：UNP residues 260-632
Not recorded No recorded non-water small molecule 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
5XFL Crystal structure of the force-sensing device region of alpha N-catenin Deposited 2017-04-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 260–632（373 aa） Fragment：UNP residues 260-632
Not recorded No recorded non-water small molecule 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
5XFL Crystal structure of the force-sensing device region of alpha N-catenin Deposited 2017-04-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 260–632（373 aa） Fragment：UNP residues 260-632
Not recorded No recorded non-water small molecule 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
5XFL Crystal structure of the force-sensing device region of alpha N-catenin Deposited 2017-04-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 260–632（373 aa） Fragment：UNP residues 260-632
Not recorded No recorded non-water small molecule 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
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 ligand/ion 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 15–263； UniProt 13–261 Author chain B； PDBConstruct 15–263； UniProt 13–261 Author chain C； PDBConstruct 15–263； UniProt 13–261 Author chain D； PDBConstruct 15–263； UniProt 13–261

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 4p9t

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4p9t
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4p9t
Deposition date deposition_date2014-04-04
Structure title titleStructure of the free form of the N-terminal VH1 domain of monomeric alpha-catenin
Keywords keywordsCytoskeletal protein, adherens junction, helix bundle, 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_guinier38.16 Å
Radius of gyration Rg (electron density) rg_electron37.55 Å
Forward intensity I(0) i0166536000.00
Molecular weight molecular_weight97745.0 kDa
Excluded volume excluded_volume119320 ų
Envelope volume envelope_volume168360 ų
Hydration-shell volume shell_volume39556 ų
Envelope diameter envelope_diameter135.9 Å
Shell Rg shell_rg41.17 Å
Envelope Rg envelope_rg36.50 Å
Shape Rg shape_rg37.51 Å
Total Rg total_rg37.89 Å
Total atoms total_atoms6693
Residues n_residues924
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 dmax126.8 Å
Rg (real space) rg_real38.18 Å
Rg uncertainty (real space) rg_real_error1.25 Å
I(0) (real space) i0_real1.6650e+08
I(0) uncertainty (real space) i0_real_error3.1540e+06
Rg (reciprocal space) rg_reciprocal38.17 Å
I(0) (reciprocal space) i0_reciprocal166500000.0000
Solution quality estimate total_estimate0.6699
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.3 Å
Skewness Skewness skewness0.275
Kurtosis Kurtosis kurtosis-0.430
Angular range angular_range— – 0.2050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5845000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 0.035; Positv: 1.000; Valcen: 0.994; Smooth: 0.839
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id4p9tA01
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_id4p9tA02
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_id4p9tB01
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_id4p9tB02
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_id4p9tC01
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_id4p9tC02
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_id4p9tD01
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_id4p9tD02
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)