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6y6e

drosophila Unr CSD456

Method: X-RAY DIFFRACTION Dmax: 93.1 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Upstream of N-ras, isoform A

Drosophila melanogaster

UniProt Q9VSK3

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 424–677 Not recorded EMC ETHYL MERCURY ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M tri-sodium citrate (pH 5.5), 20% PEG2000 Resolution 2.02 Å R-free 0.251

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 6Y6E Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4QQB Structural basis for the assembly of the SXL-UNR translation regulatory complex Deposited 2014-06-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric
Chain X 185–252（68 aa） Fragment：CSD1, UNP residues 185-252
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M LiSO4, PEG3350 1-5 %, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.236
4QQB Structural basis for the assembly of the SXL-UNR translation regulatory complex Deposited 2014-06-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric
Chain Y 185–252（68 aa） Fragment：CSD1, UNP residues 185-252
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M LiSO4, PEG3350 1-5 %, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.236
6Y4H Solution structure of cold-shock domain 7 and 8 of drosophila Upstream of N-Ras (Unr) Deposited 2020-02-21 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 756–922（167 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N] dCSD78, 150 mM sodium chloride, 20 mM sodium phosphate, 1 mM DTT, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N] dCSD78, 150 mM sodium chloride, 20 mM sodium phosphate, 1 mM DTT, 100% D2O | 100% D2O
Resolution not provided
6Y6M solution structure of cold-shock domain 1 and 2 of drosophila Upstream of N-Ras (Unr) Deposited 2020-02-26 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 186–344（159 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.4；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition 50 mM sodium chloride, 20 mM sodium phosphate, 10 mM DTT, 0.3 mM [U-99% 13C; U-99% 15N] protein, 0.36 mM RNA, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 50 mM sodium chloride, 20 mM sodium phosphate, 10 mM DTT, 0.3 mM [U-99% 13C; U-99% 15N] protein, 0.36 mM RNA, 100% D2O | 100% D2O
Resolution not provided
6Y96 solution structure of cold-shock domain 9 of drosophila Upstream of N-Ras (Unr) Deposited 2020-03-06 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 899–990（92 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition 0.24 mM [U-99% 13C; U-99% 15N] protein, 50 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.24 mM [U-99% 13C; U-99% 15N] protein, 50 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 100% D2O | 100% D2O
Resolution not provided
7ZHH Complex structure of drosophila Unr CSD789 and a poly(A) RNA sequence Deposited 2022-04-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 756–990（235 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M Tris-Cl (pH 7.0) 0.2 M lithium sulfate 2 M ammonium sulfate
Resolution 1.60 Å R-free 0.210
7ZHR Complex structure of drosophila Unr CSD789 and pAbp RRM3 Deposited 2022-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 756–990（235 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M sodium formate 0.1 M bis-tris propane 20 % (w/v) PEG 3350
Resolution 2.99 Å R-free 0.315

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9VSK3_DROME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–257； UniProt 424–677

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 6y6e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6y6e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6y6e
Deposition date deposition_date2020-02-26
Structure title titledrosophila Unr CSD456
Keywords keywordsCSD, ncCSD, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.85 Å
Radius of gyration Rg (electron density) rg_electron25.62 Å
Forward intensity I(0) i014001700.00
Molecular weight molecular_weight26954.0 kDa
Excluded volume excluded_volume33003 ų
Envelope volume envelope_volume43566 ų
Hydration-shell volume shell_volume16482 ų
Envelope diameter envelope_diameter94.8 Å
Shell Rg shell_rg29.00 Å
Envelope Rg envelope_rg25.85 Å
Shape Rg shape_rg25.54 Å
Total Rg total_rg26.28 Å
Total atoms total_atoms1849
Residues n_residues238
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 dmax93.1 Å
Rg (real space) rg_real26.27 Å
Rg uncertainty (real space) rg_real_error1.11 Å
I(0) (real space) i0_real1.4000e+07
I(0) uncertainty (real space) i0_real_error2.3060e+05
Rg (reciprocal space) rg_reciprocal26.14 Å
I(0) (reciprocal space) i0_reciprocal14000000.0000
Solution quality estimate total_estimate0.7385
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.8 Å
Skewness Skewness skewness0.608
Kurtosis Kurtosis kurtosis-0.369
Angular range angular_range— – 0.3050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2755000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.467; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.224; Smooth: 0.973
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id6y6eA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
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8. Citations (1)

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9. Files and Curves (10)