SAXSdb — 4apt

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

ATAXIN-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 566–688 Chain B； UniProt 566–688	Fragment：AXH DOMAIN, RESIDUES 566-688	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：PROTEIN SAMPLES AT 20 MG/ML CRYSTALLISED IN 0.4 M POTASSIUM SODIUM TARTRATE AT ROOM TEMPERATURE.	Resolution 2.50 Å R-free 0.288
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 566–688 Chain D； UniProt 566–688	Fragment：AXH DOMAIN, RESIDUES 566-688	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：PROTEIN SAMPLES AT 20 MG/ML CRYSTALLISED IN 0.4 M POTASSIUM SODIUM TARTRATE AT ROOM TEMPERATURE.	Resolution 2.50 Å R-free 0.288

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 4APT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OA8 AXH domain of human spinocerebellar ataxin-1 Deposited 2003-01-02	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 563–694（132 aa） Fragment：AXH DOMAIN, RESIDUES 562-694 Chain B 563–694（132 aa） Fragment：AXH DOMAIN, RESIDUES 562-694	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；PROTEIN WAS CRYSTALLIZED FROM 0.1M TRIS/HCL, PH 7.0, 0.2M AMMONIUM SULPHATE, 5 MM DTT, 15% PEG 4000, 20% GLYCEROL, AT 290K	Resolution 1.70 Å R-free 0.252
1OA8 AXH domain of human spinocerebellar ataxin-1 Deposited 2003-01-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 563–694（132 aa） Fragment：AXH DOMAIN, RESIDUES 562-694 Chain D 563–694（132 aa） Fragment：AXH DOMAIN, RESIDUES 562-694	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；PROTEIN WAS CRYSTALLIZED FROM 0.1M TRIS/HCL, PH 7.0, 0.2M AMMONIUM SULPHATE, 5 MM DTT, 15% PEG 4000, 20% GLYCEROL, AT 290K	Resolution 1.70 Å R-free 0.252
2M41 Solution Structure of the AXH domain of Ataxin-1 in complex with ligand peptide from Capicua Deposited 2013-01-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 566–688（123 aa） Fragment：AXH domain, native residues A567-K689	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；310 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] Ataxin-1 AXH domain, 0.6 mM CIC polypeptide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-100% 15N] Ataxin-1 AXH domain, 0.6 mM CIC polypeptide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4AQP The structure of the AXH domain of ataxin-1. Deposited 2012-04-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 566–688（123 aa） Fragment：AXH DOMAIN, RESIDUES 566-688 Chain B 566–688（123 aa） Fragment：AXH DOMAIN, RESIDUES 566-688	Not recorded	NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PROTEIN SAMPLES AT 20 MG/ML CRYSTALLISED IN 0.1 M MES, PH 6.5, 10% W/V PWG 20000 AT ROOM TEMPERATURE.	Resolution 2.45 Å R-free 0.267
4AQP The structure of the AXH domain of ataxin-1. Deposited 2012-04-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 566–688（123 aa） Fragment：AXH DOMAIN, RESIDUES 566-688 Chain D 566–688（123 aa） Fragment：AXH DOMAIN, RESIDUES 566-688	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PROTEIN SAMPLES AT 20 MG/ML CRYSTALLISED IN 0.1 M MES, PH 6.5, 10% W/V PWG 20000 AT ROOM TEMPERATURE.	Resolution 2.45 Å R-free 0.267
4J2J Crystal structure of AXH domain complex with Capicua Deposited 2013-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 562–688（127 aa） Fragment：AXH domain, UNP residues 562-688	Mutation：I580M,I605M 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 8；293 K；0.1M Calcium chloride, 24%(v/v) PEG3350, 4%(v/v) pentaerythritol ethoxylate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.270
4J2J Crystal structure of AXH domain complex with Capicua Deposited 2013-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 562–688（127 aa） Fragment：AXH domain, UNP residues 562-688	Mutation：I580M,I605M 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 8；293 K；0.1M Calcium chloride, 24%(v/v) PEG3350, 4%(v/v) pentaerythritol ethoxylate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.270
4J2J Crystal structure of AXH domain complex with Capicua Deposited 2013-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 562–688（127 aa） Fragment：AXH domain, UNP residues 562-688	Mutation：I580M,I605M 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 8；293 K；0.1M Calcium chloride, 24%(v/v) PEG3350, 4%(v/v) pentaerythritol ethoxylate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.270
4J2L Crystal Structure of AXH domain complexed with Capicua Deposited 2013-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 562–688（127 aa） Fragment：AXH domain, UNP residues 562-688	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.6M NaCl, 3%(v/v) glycerol, 16%(w/v) PEG3350, 1mM L-Glutathione, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.15 Å R-free 0.294
4J2L Crystal Structure of AXH domain complexed with Capicua Deposited 2013-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 562–688（127 aa） Fragment：AXH domain, UNP residues 562-688	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.6M NaCl, 3%(v/v) glycerol, 16%(w/v) PEG3350, 1mM L-Glutathione, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.15 Å R-free 0.294

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

View Construct and Data Evidence

UniProt name	ATX1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–126； UniProt 566–688 Author chain B； PDBConstruct 4–126； UniProt 566–688 Author chain C； PDBConstruct 4–126； UniProt 566–688 Author chain D； PDBConstruct 4–126； UniProt 566–688

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	4apt
Deposition date deposition_date	2012-04-05
Structure title title	The structure of the AXH domain of ataxin-1.
Keywords keywords	RNA BINDING PROTEIN, RNA BINDING, OB-FOLD, HIGH MOBILITY GROUP HOMOLOGY, HMG, DIMERIZATION; RNA BINDING PROTEIN
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	27.05 Å
Radius of gyration Rg (electron density) rg_electron	26.19 Å
Forward intensity I(0) i0	47738200.00
Molecular weight molecular_weight	54628.0 kDa
Excluded volume excluded_volume	68799 Å³
Envelope volume envelope_volume	84163 Å³
Hydration-shell volume shell_volume	27679 Å³
Envelope diameter envelope_diameter	90.0 Å
Shell Rg shell_rg	32.72 Å
Envelope Rg envelope_rg	26.19 Å
Shape Rg shape_rg	26.18 Å
Total Rg total_rg	26.97 Å
Total atoms total_atoms	3836
Residues n_residues	499
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	89.4 Å
Rg (real space) rg_real	27.17 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	4.7740e+07
I(0) uncertainty (real space) i0_real_error	7.5970e+05
Rg (reciprocal space) rg_reciprocal	27.13 Å
I(0) (reciprocal space) i0_reciprocal	47740000.0000
Solution quality estimate total_estimate	0.8543
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.8 Å
Skewness Skewness skewness	0.460
Kurtosis Kurtosis kurtosis	-0.418
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24530000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.743; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.951

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	ATAXIN-1
Molecular weight formula_weight	13776.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3881

GAMAPPTLPPYFMKGSIIQLANGELKKVEDLKTEDFIQSAEISNDLKIDSSTVERIEDSHSPGVAVIQFAVGEHRAQVSVEVLVEYPFFVFGQGWSSCCPERTSQLFDLPCSKLSVGDVCISLTLK

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	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	45

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4apta1
Class class	b — All beta proteins
Fold Fold fold	b.145 — AXH domain
Superfamily Superfamily superfamily	b.145.1 — AXH domain
Family Family family	b.145.1.1 — AXH domain

Domain ID domain_id	d4apta2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4aptb1
Class class	b — All beta proteins
Fold Fold fold	b.145 — AXH domain
Superfamily Superfamily superfamily	b.145.1 — AXH domain
Family Family family	b.145.1.1 — AXH domain

Domain ID domain_id	d4aptb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4aptc1
Class class	b — All beta proteins
Fold Fold fold	b.145 — AXH domain
Superfamily Superfamily superfamily	b.145.1 — AXH domain
Family Family family	b.145.1.1 — AXH domain

Domain ID domain_id	d4aptc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4aptd1
Class class	b — All beta proteins
Fold Fold fold	b.145 — AXH domain
Superfamily Superfamily superfamily	b.145.1 — AXH domain
Family Family family	b.145.1.1 — AXH domain

Domain ID domain_id	d4aptd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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8. Citations (4)

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Unit-cell length a length_a	41.470 Å
Unit-cell length b length_b	80.830 Å
Unit-cell length c length_c	139.960 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	40.406 Å
R factor r_factor	0.2385
R_work r_work	0.2358
R_free r_free	0.2882

fit	/app/data/saxs_computation/ap/4apt/4apt.fit
pddf	/app/data/pr_computation/ap/4apt/4apt.pr.out
profile	/app/data/saxs_computation/ap/4apt/4apt.dat

The structure of the AXH domain of ataxin-1.

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

ATAXIN-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