SAXSdb — 2lcc

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

AT-rich interactive domain-containing protein 4A

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 568–635	Fragment：UNP RESIDUES 568-635	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 0.4；Pressure ambient NMR sample composition：0.5 mM [U-95% 15N] entity-1, 50 mM sodium phosphate-2, 50 mM sodium chloride-3, 5 mM DTT-4, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.5 mM [U-95% 13C; U-95% 15N] entity-5, 50 mM sodium phosphate-6, 50 mM sodium chloride-7, 5 mM DTT-8, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 2LCC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2MAM Solution structure of the interdigitated double Tudor domain of RBBP1 Deposited 2013-07-15	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–121（118 aa） Fragment：UNP RESIDUES 4-121	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.8；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition 0.6 mM [U-95% 13C; U-95% 15N] entity-1, 10 % [U-99% 2H] D2O-2, 0.0004 % DSS-3, 15 mM DTT-4, 50 mM sodium chloride-5, 50 mM TRIS-6, 2 mM EDTA-7, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2YRV Solution structure of the RBB1NT domain of human RB(retinoblastoma)-binding protein 1 Deposited 2007-04-03	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 170–273（104 aa） Fragment：UNP region 170-273	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.2mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
6BPH Crystal structure of the chromodomain of RBBP1 Deposited 2017-11-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 568–635（68 aa）	Not recorded	UNX UNKNOWN LIGAND × 34	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG 3350, 0.2M magnesium chloride, 0.1M HEPES, pH 7.5	Resolution 1.85 Å R-free 0.226
6L87 Solution structure of the tandem PWWP-ARID domains of human RBBP1 Deposited 2019-11-05	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 171–414（244 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；302 K；Ionic strength (raw mmCIF value) 720；Pressure 1 NMR sample composition 10 mM sodium phosphate, 700 mM sodium chloride, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 10 mM sodium phosphate, 700 mM sodium chloride, 1 mM EDTA, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
7SMC p107 pocket domain complexed with ARID4A peptide Deposited 2021-10-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 953–967（15 aa） Fragment：UNP residues 953-967	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate	Resolution 2.70 Å R-free 0.298
7SMC p107 pocket domain complexed with ARID4A peptide Deposited 2021-10-25	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 953–967（15 aa） Fragment：UNP residues 953-967	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate	Resolution 2.70 Å R-free 0.298
7V8N Crystal structure of the PWWP-ARID domain of ARID4A Deposited 2021-08-23	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 169–417（249 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.4 M ammonium phosphate dibasic, 0.1 M Tris pH8.0	Resolution 2.05 Å R-free 0.231
7V8N Crystal structure of the PWWP-ARID domain of ARID4A Deposited 2021-08-23	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 169–417（249 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.4 M ammonium phosphate dibasic, 0.1 M Tris pH8.0	Resolution 2.05 Å R-free 0.231

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

View Construct and Data Evidence

UniProt name	ARI4A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–68； UniProt 568–635

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	2lcc
Deposition date deposition_date	2011-04-28
Structure title title	Solution structure of RBBP1 chromobarrel domain
Keywords keywords	chromobarrel domain, RBBP1, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	15.02 Å
Radius of gyration Rg (electron density) rg_electron	14.00 Å
Forward intensity I(0) i0	464722000.00
Molecular weight molecular_weight	181240.0 kDa
Excluded volume excluded_volume	226470 Å³
Envelope volume envelope_volume	48761 Å³
Hydration-shell volume shell_volume	20932 Å³
Envelope diameter envelope_diameter	58.2 Å
Shell Rg shell_rg	25.86 Å
Envelope Rg envelope_rg	19.55 Å
Shape Rg shape_rg	14.00 Å
Total Rg total_rg	14.39 Å
Total atoms total_atoms	25300
Residues n_residues	1520
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	54.3 Å
Rg (real space) rg_real	15.04 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	4.6470e+08
I(0) uncertainty (real space) i0_real_error	5.9360e+06
Rg (reciprocal space) rg_reciprocal	15.04 Å
I(0) (reciprocal space) i0_reciprocal	464700000.0000
Solution quality estimate total_estimate	0.8513
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.2 Å
Skewness Skewness skewness	0.358
Kurtosis Kurtosis kurtosis	-0.172
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	230900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.736; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.865; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2lccA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

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8. Citations (1)

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Description description	AT-rich interactive domain-containing protein 4A
Molecular weight formula_weight	9082.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	25300

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

fit	/app/data/saxs_computation/lc/2lcc/2lcc.fit
pddf	/app/data/pr_computation/lc/2lcc/2lcc.pr.out
profile	/app/data/saxs_computation/lc/2lcc/2lcc.dat

Solution structure of RBBP1 chromobarrel domain

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

AT-rich interactive domain-containing protein 4A

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)