SAXSdb — 4igg

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Catenin alpha-1

Homo sapiens

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 82–906 Chain B； UniProt 82–906	Fragment：UNP residues 82-906	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.8；295 K；0.9 M Na/K Phosphate, 0.3 M Na Malonate, pH 6.8, VAPOR DIFFUSION, temperature 295K	Resolution 3.66 Å R-free 0.241

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 4IGG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1H6G alpha-catenin M-domain Deposited 2001-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 377–632（256 aa） Fragment：M-FRAGMENT, RESIDUES 377-632	Non-standard monomer：Yes (specific site not provided by mmCIF)	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；30 % (V/V) MPD, 0.1 M SODIUM ACETETE BUFFER, PH 4.6, 20 MM CALCIUM CHLORIDE	Resolution 2.20 Å R-free 0.257
1H6G alpha-catenin M-domain Deposited 2001-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 377–632（256 aa） Fragment：M-FRAGMENT, RESIDUES 377-632	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；30 % (V/V) MPD, 0.1 M SODIUM ACETETE BUFFER, PH 4.6, 20 MM CALCIUM CHLORIDE	Resolution 2.20 Å R-free 0.257
1L7C alpha-catenin fragment, residues 385-651 Deposited 2002-03-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 385–651（267 aa） Fragment：Residues 385-651	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 4；293 K；sodium acetate, dithiothreitol, urea, sodium/potassium tartrate, isopropanol, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.273
1L7C alpha-catenin fragment, residues 385-651 Deposited 2002-03-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 385–651（267 aa） Fragment：Residues 385-651	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 4；293 K；sodium acetate, dithiothreitol, urea, sodium/potassium tartrate, isopropanol, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.273
1L7C alpha-catenin fragment, residues 385-651 Deposited 2002-03-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 385–651（267 aa） Fragment：Residues 385-651	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 4；293 K；sodium acetate, dithiothreitol, urea, sodium/potassium tartrate, isopropanol, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.273
1L7C alpha-catenin fragment, residues 385-651 Deposited 2002-03-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 385–651（267 aa） Fragment：Residues 385-651 Chain C 385–651（267 aa） Fragment：Residues 385-651	Non-standard monomer：Yes (specific site not provided by mmCIF) 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 4；293 K；sodium acetate, dithiothreitol, urea, sodium/potassium tartrate, isopropanol, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.273
4EHP Crystal Structure of human vinculin head domain (residues 1-252) in complex with alpha-catenin (residues 277-382) Deposited 2012-04-03	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 277–382（106 aa） Fragment：unp residues 277-382	Not recorded	ACT ACETATE ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；295 K；PEG 3350, sodium acetate, VAPOR DIFFUSION, temperature 295K	Resolution 2.66 Å R-free 0.229
6UPV Alpha-E-catenin ABD-F-actin complex Deposited 2019-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain L 1–906（906 aa） Chain M 1–906（906 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7UTJ Cryogenic electron microscopy 3D map of F-actin bound by human dimeric alpha-catenin Deposited 2022-04-27	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 G 22–906（885 aa） Chain H 22–906（885 aa） Chain I 22–906（885 aa） Chain K 22–906（885 aa） Chain L 22–906（885 aa） Chain Z 22–906（885 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.77 Å
9BL2 KIR3DL1001 in complex with HLA-B57:03 presenting the AW10 peptide Deposited 2024-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 850–859（10 aa） Fragment：residues 850-859 (Uniprot numbering)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；18% PEG-3350, 2% tacsimate pH 5.0, 0.1 M tri-sodium citrate pH 5.6	Resolution 2.10 Å R-free 0.231
9BL3 KIR3DL1114 in complex with HLA-B57:03 presenting the AW10 peptide Deposited 2024-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 850–859（10 aa） Fragment：residues 850-859 (Uniprot numbering)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；16% PEG 3350, 2% tacsimate pH 5.0, 0.1 M tri-sodium citrate pH 5.6	Resolution 2.00 Å R-free 0.229
9BL4 KIR3DL1086 in complex with HLA-B57:03 presenting the AW10 peptide Deposited 2024-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 850–859（10 aa） Fragment：residues 850-859 (Uniprot numbering)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；16% PEG 3350, 2% tacsimate pH 5.0, 0.1 M tri-sodium citrate pH 5.6	Resolution 1.75 Å R-free 0.227

8 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CTNA1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–825； UniProt 82–906 Author chain B； PDBConstruct 1–825； UniProt 82–906

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4igg
Deposition date deposition_date	2012-12-17
Structure title title	Full-length human alpha-catenin crystal structure
Keywords keywords	Asymmetric dimer, adherens junctions, F-actin binding, CELL ADHESION; CELL ADHESION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	38.56 Å
Radius of gyration Rg (electron density) rg_electron	38.23 Å
Forward intensity I(0) i0	449597000.00
Molecular weight molecular_weight	167590.0 kDa
Excluded volume excluded_volume	208340 Å³
Envelope volume envelope_volume	278430 Å³
Hydration-shell volume shell_volume	60688 Å³
Envelope diameter envelope_diameter	138.4 Å
Shell Rg shell_rg	44.21 Å
Envelope Rg envelope_rg	37.88 Å
Shape Rg shape_rg	38.25 Å
Total Rg total_rg	38.51 Å
Total atoms total_atoms	11714
Residues n_residues	1521
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	128.1 Å
Rg (real space) rg_real	38.48 Å
Rg uncertainty (real space) rg_real_error	1.06 Å
I(0) (real space) i0_real	4.4960e+08
I(0) uncertainty (real space) i0_real_error	6.4150e+06
Rg (reciprocal space) rg_reciprocal	38.53 Å
I(0) (reciprocal space) i0_reciprocal	449600000.0000
Solution quality estimate total_estimate	0.8735
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	50.0 Å
Skewness Skewness skewness	0.330
Kurtosis Kurtosis kurtosis	-0.184
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	64830000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.843

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Catenin alpha-1
Molecular weight formula_weight	92208.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	11714

ESQFLKEELVAAVEDVRKQGDLMKAAAGEFADDPCSSVKRGNMVRAARALLSAVTRLLILADMADVYKLLVQLKVVEDGILKLRNAGNEQDLGIQYKALKPEVDKLNIMAAKRQQELKDVGHRDQMAAARGILQKNVPILYTASQACLQHPDVAAYKANRDLIYKQLQQAVTGISNAAQATASDDASQHQGGGGGELAYALNNFDKQIIVDPLSFSEERFRPSLEERLESIISGAALMADSSCTRDDRRERIVAECNAVRQALQDLLSEYMGNAGRKERSDALNSAIDKMTKKTRDLRRQLRKAVMDHVSDSFLETNVPLLVLIEAAKNGNEKEVKEYAQVFREHANKLIEVANLACSISNNEEGVKLVRMSASQLEALCPQVINAALALAAKPQSKLAQENMDLFKEQWEKQVRVLTDAVDDITSIDDFLAVSENHILEDVNKCVIALQEKDVDGLDRTAGAIRGRAARVIHVVTSEMDNYEPGVYTEKVLEATKLLSNTVMPRFTEQVEAAVEALSSDPAQPMDENEFIDASRLVYDGIRDIRKAVLMIRTPEELDDSDFETEDFDVRSRTSVQTEDDQLIAGQSARAIMAQLPQEQKAKIAEQVASFQEEKSKLDAEVSKWDDSGNDIIVLAKQMCMIMMEMTDFTRGKGPLKNTSDVISAAKKIAEAGSRMDKLGRTIADHCPDSACKQDLLAYLQRIALYCHQLNICSKVKAEVQNLGGELVVSGVDSAMSLIQAAKNLMNAVVQTVKASYVASTKYQKSQGMASLNLPAVSWKMKAPEKKPLVKREKQDETQTKIKRASQKKHVNPVQALSEFKAMDSIPHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	4iggA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	160 — HR1 repeat

Domain ID domain_id	4iggA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	230 — Alpha-catenin/vinculin-like

Domain ID domain_id	4iggA04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	230 — Alpha-catenin/vinculin-like

Domain ID domain_id	4iggA05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	230 — Alpha-catenin/vinculin-like

Domain ID domain_id	4iggA06
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	230 — Alpha-catenin/vinculin-like

Domain ID domain_id	4iggB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	160 — HR1 repeat

Domain ID domain_id	4iggB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	230 — Alpha-catenin/vinculin-like

Domain ID domain_id	4iggB04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	230 — Alpha-catenin/vinculin-like

Domain ID domain_id	4iggB05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	230 — Alpha-catenin/vinculin-like

Domain ID domain_id	4iggB06
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	230 — Alpha-catenin/vinculin-like

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8. Citations (1)

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Unit-cell length a length_a	145.629 Å
Unit-cell length b length_b	145.629 Å
Unit-cell length c length_c	139.081 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	3.660 Å
Low-resolution limit resolution_low	23.210 Å
R factor r_factor	0.2187
R_work r_work	0.2175
R_free r_free	0.2413

fit	/app/data/saxs_computation/ig/4igg/4igg.fit
pddf	/app/data/pr_computation/ig/4igg/4igg.pr.out
profile	/app/data/saxs_computation/ig/4igg/4igg.dat

Full-length human alpha-catenin crystal structure

1. Protein Identity and Related Structures Protein Identity & Related Structures

Catenin alpha-1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction