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6y4h

Solution structure of cold-shock domain 7 and 8 of drosophila Upstream of N-Ras (Unr)

Method: SOLUTION NMR Dmax: 63.5 Å Quality: GOOD
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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 756–922 Not recorded No other associated polymer 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

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 6Y4H 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 experimental method 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 experimental method 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
6Y6E drosophila Unr CSD456 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 424–677（254 aa）
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
6Y6M solution structure of cold-shock domain 1 and 2 of drosophila Upstream of N-Ras (Unr) Deposited 2020-02-26 Different construct Different experimental conditions 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 experimental conditions 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 method 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 experimental method 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 2–168； UniProt 756–922

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 6y4h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6y4h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6y4h
Deposition date deposition_date2020-02-21
Structure title titleSolution structure of cold-shock domain 7 and 8 of drosophila Upstream of N-Ras (Unr)
Keywords keywordsCSD, ncCSD, 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_guinier18.02 Å
Radius of gyration Rg (electron density) rg_electron17.72 Å
Forward intensity I(0) i02040870000.00
Molecular weight molecular_weight372620.0 kDa
Excluded volume excluded_volume461700 ų
Envelope volume envelope_volume51799 ų
Hydration-shell volume shell_volume21276 ų
Envelope diameter envelope_diameter74.2 Å
Shell Rg shell_rg27.34 Å
Envelope Rg envelope_rg21.18 Å
Shape Rg shape_rg17.67 Å
Total Rg total_rg18.00 Å
Total atoms total_atoms51800
Residues n_residues3360
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 dmax63.5 Å
Rg (real space) rg_real18.05 Å
Rg uncertainty (real space) rg_real_error0.58 Å
I(0) (real space) i0_real2.0410e+09
I(0) uncertainty (real space) i0_real_error2.9650e+07
Rg (reciprocal space) rg_reciprocal18.05 Å
I(0) (reciprocal space) i0_reciprocal2041000000.0000
Solution quality estimate total_estimate0.7698
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary19.7 Å
Skewness Skewness skewness0.411
Kurtosis Kurtosis kurtosis-0.191
Angular range angular_range— – 0.4400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1325000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.687; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; 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_id6y4hA01
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)