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1s4j

NMR structure of cross-reactive peptides from Homo sapiens

Method: SOLUTION NMR Dmax: 16.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

60S acidic ribosomal protein P2

OrganismNot specified

UniProt P05387

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 103–115 Fragment：h13 - C-terminal domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 5.5；278 K；Ionic strength (raw mmCIF value) 10mM phosphate buffer；Pressure ambient NMR sample composition：2mM of peptide; 10% D2O; 10mM phosphate buffer at pH 5.5 | 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 1S4J Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2LBF Solution structure of the dimerization domain of human ribosomal protein P1/P2 heterodimer Deposited 2011-03-30 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–69（69 aa） Fragment：UNP residues 1-69
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] protein_1-1, 1 mM [U-100% 13C; U-100% 15N] protein_2-2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2W1O NMR structure of dimerization domain of human ribosomal protein P2 Deposited 2008-10-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–69（69 aa） Fragment：RESIDUES 1-69
Chain B 1–69（69 aa） Fragment：RESIDUES 1-69
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 200MM SODIUM SULFATE；Pressure 1.0
NMR sample composition 90% WATER / 10% D2O
Resolution not provided
4BEH Solution structure of human ribosomal protein P1.P2 heterodimer Deposited 2013-03-10 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–115（115 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1.0
NMR sample composition 10% WATER/90% D2O
Resolution not provided
4V6X Structure of the human 80S ribosome Deposited 2013-02-27 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 84 PDB declaration: 89-meric
Chain Cu 1–115（115 aa）
Chain Cv 1–115（115 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds using two pieces of filter paper, then plunge into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.00 Å
5DDZ Crystal structure of the RTA-c10-P2 complex Deposited 2015-08-25 Different construct 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 106–115（10 aa） Fragment：UNP residues 106-115
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.4 M ammonium dihydrogen phosphate
Resolution 1.50 Å R-free 0.175

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

View Construct and Data Evidence
UniProt name RLA2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–13； UniProt 103–115

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 1s4j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1s4j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1s4j
Deposition date deposition_date2004-01-16
Structure title titleNMR structure of cross-reactive peptides from Homo sapiens
Keywords keywordsantigenic peptide, ribosomal p2 protein, Chagas disease, RIBOSOME; RIBOSOME
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier5.74 Å
Radius of gyration Rg (electron density) rg_electron6.11 Å
Forward intensity I(0) i016631400.00
Molecular weight molecular_weight29409.0 kDa
Excluded volume excluded_volume34536 ų
Envelope volume envelope_volume3215 ų
Hydration-shell volume shell_volume4168 ų
Envelope diameter envelope_diameter25.8 Å
Shell Rg shell_rg11.94 Å
Envelope Rg envelope_rg7.74 Å
Shape Rg shape_rg6.08 Å
Total Rg total_rg6.48 Å
Total atoms total_atoms3620
Residues n_residues260
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 dmax16.8 Å
Rg (real space) rg_real5.63 Å
Rg uncertainty (real space) rg_real_error0.02 Å
I(0) (real space) i0_real1.6510e+07
I(0) uncertainty (real space) i0_real_error9.2550e+04
Rg (reciprocal space) rg_reciprocal5.77 Å
I(0) (reciprocal space) i0_reciprocal16630000.0000
Solution quality estimate total_estimate0.7308
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary7.2 Å
Skewness Skewness skewness0.108
Kurtosis Kurtosis kurtosis-0.580
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha2.6030
Highest regularization parameter α highest_alpha617.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.994; Stabil: 0.917; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.798
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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

SCOP 2.08 (1 domains)

Domain ID domain_idd1s4ja_
Class classj — Peptides
Fold Fold foldj.111 — Cross-reactive peptides from 60S acidic ribosomal protein p2
Superfamily Superfamily superfamilyj.111.1 — Cross-reactive peptides from 60S acidic ribosomal protein p2
Family Family familyj.111.1.1 — Cross-reactive peptides from 60S acidic ribosomal protein p2
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8. Citations (1)

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9. Files and Curves (10)