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2yrv

Solution structure of the RBB1NT domain of human RB(retinoblastoma)-binding protein 1

Method: SOLUTION NMR Dmax: 54.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

AT-rich interactive domain-containing protein 4A

Homo sapiens

UniProt P29374

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 170–273 Fragment：UNP region 170-273 No other associated polymer 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

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 2YRV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2LCC Solution structure of RBBP1 chromobarrel domain Deposited 2011-04-28 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 568–635（68 aa） Fragment：UNP RESIDUES 568-635
Not recorded No recorded non-water small molecule 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
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
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 8–111； UniProt 170–273

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 2yrv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2yrv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2yrv
Deposition date deposition_date2007-04-03
Structure title titleSolution structure of the RBB1NT domain of human RB(retinoblastoma)-binding protein 1
Keywords keywords;ARID domain-containing protein 4A, Retinoblastoma-binding protein 1, RBBP-1, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, TRANSCRIPTION ;; TRANSCRIPTION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.36 Å
Radius of gyration Rg (electron density) rg_electron14.60 Å
Forward intensity I(0) i0885871000.00
Molecular weight molecular_weight255150.0 kDa
Excluded volume excluded_volume320960 ų
Envelope volume envelope_volume40233 ų
Hydration-shell volume shell_volume18157 ų
Envelope diameter envelope_diameter60.8 Å
Shell Rg shell_rg24.98 Å
Envelope Rg envelope_rg19.50 Å
Shape Rg shape_rg14.57 Å
Total Rg total_rg14.93 Å
Total atoms total_atoms36080
Residues n_residues2340
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 dmax54.9 Å
Rg (real space) rg_real15.31 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real8.8590e+08
I(0) uncertainty (real space) i0_real_error1.1520e+07
Rg (reciprocal space) rg_reciprocal15.32 Å
I(0) (reciprocal space) i0_reciprocal885900000.0000
Solution quality estimate total_estimate0.7566
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary18.8 Å
Skewness Skewness skewness0.288
Kurtosis Kurtosis kurtosis-0.062
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha382500.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.622; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.000
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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_id2yrvA01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily140 —
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8. Citations (1)

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9. Files and Curves (10)