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2lli

Low resolution structure of RNA-binding subunit of the TRAMP complex

Method: SOLUTION NMR Dmax: 103.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein AIR2

Saccharomyces cerevisiae

UniProt Q12476

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 57–180 Fragment：UNP residues 57-180 ZN ZINC ION × 5 SOLUTION NMR NMR measurement conditions：pH 8；293 K；Ionic strength (raw mmCIF value) 0.5；Pressure ambient NMR sample composition：100 uM uM [U-99% 13C; U-99% 15N] protein_1, 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 2LLI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3NYB Structure and function of the polymerase core of TRAMP, a RNA surveillance complex Deposited 2010-07-14 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 118–198（81 aa） Fragment：fourth and fifth zinc knuckles of Air2p (UNP residues 118-198)
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；100 mM sodium citrate at pH 5.8, 200 mM sodium acetate, 11% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.258
4U4C The molecular architecture of the TRAMP complex reveals the organization and interplay of its two catalytic activities Deposited 2014-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: Dimeric
Chain B 1–62（62 aa） Fragment：UNP residues 1-62,UNP residues 111-160,UNP residues 1-62,UNP residues 111-160
Not recorded SO4 SULFATE ION × 7 EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 2 PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；285.15 K；0.1 M Tris pH 8.2, 0.15 M Li2SO4, 32% PEG 400
Resolution 2.40 Å R-free 0.240

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AIR2_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–124； UniProt 57–180

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 2lli

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2lli
Deposition date deposition_date2011-11-10
Structure title titleLow resolution structure of RNA-binding subunit of the TRAMP complex
Keywords keywordsRNA surveillance, RNA degradation, RNA binding, exosome, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier38.48 Å
Radius of gyration Rg (electron density) rg_electron40.50 Å
Forward intensity I(0) i01483700000.00
Molecular weight molecular_weight291030.0 kDa
Excluded volume excluded_volume351720 ų
Envelope volume envelope_volume472320 ų
Hydration-shell volume shell_volume81394 ų
Envelope diameter envelope_diameter204.5 Å
Shell Rg shell_rg49.74 Å
Envelope Rg envelope_rg53.17 Å
Shape Rg shape_rg40.63 Å
Total Rg total_rg40.43 Å
Total atoms total_atoms39260
Residues n_residues2480
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 dmax103.8 Å
Rg (real space) rg_real34.80 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real1.4060e+09
I(0) uncertainty (real space) i0_real_error1.6620e+07
Rg (reciprocal space) rg_reciprocal39.03 Å
I(0) (reciprocal space) i0_reciprocal1482000000.0000
Solution quality estimate total_estimate0.6681
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary30.4 Å
Skewness Skewness skewness0.473
Kurtosis Kurtosis kurtosis-0.520
Angular range angular_range— – 0.2050 Å−1
Current regularization parameter α current_alpha0.9301
Highest regularization parameter α highest_alpha2693000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.002; Oscil: 0.961; Stabil: 0.985; Sysdev: 0.000; Positv: 1.000; Valcen: 0.859; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)