SAXSdb — 6y6m

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Upstream of N-ras, isoform A

Drosophila melanogaster

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 186–344	Not recorded	No other associated polymer	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

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 6Y6M	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
6Y4H Solution structure of cold-shock domain 7 and 8 of drosophila Upstream of N-Ras (Unr) Deposited 2020-02-21	Different construct Different experimental conditions	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
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
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 7–165； UniProt 186–344

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6y6m
Deposition date deposition_date	2020-02-26
Structure title title	solution structure of cold-shock domain 1 and 2 of drosophila Upstream of N-Ras (Unr)
Keywords keywords	CSD, ncCSD, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.14 Å
Radius of gyration Rg (electron density) rg_electron	24.61 Å
Forward intensity I(0) i0	2138720000.00
Molecular weight molecular_weight	368970.0 kDa
Excluded volume excluded_volume	453810 Å³
Envelope volume envelope_volume	174490 Å³
Hydration-shell volume shell_volume	46418 Å³
Envelope diameter envelope_diameter	100.7 Å
Shell Rg shell_rg	38.82 Å
Envelope Rg envelope_rg	30.22 Å
Shape Rg shape_rg	24.59 Å
Total Rg total_rg	25.07 Å
Total atoms total_atoms	50980
Residues n_residues	3300
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	84.2 Å
Rg (real space) rg_real	25.07 Å
Rg uncertainty (real space) rg_real_error	0.90 Å
I(0) (real space) i0_real	2.1390e+09
I(0) uncertainty (real space) i0_real_error	3.2110e+07
Rg (reciprocal space) rg_reciprocal	25.09 Å
I(0) (reciprocal space) i0_reciprocal	2139000000.0000
Solution quality estimate total_estimate	0.8045
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	36.1 Å
Skewness Skewness skewness	0.132
Kurtosis Kurtosis kurtosis	-0.593
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3828000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; 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_id	6y6mA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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8. Citations (1)

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Description description	Upstream of N-ras, isoform A
Molecular weight formula_weight	18494.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	50980

来源生物 organism	Drosophila melanogaster
通用名 common_name	Fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/y6/6y6m/6y6m.fit
pddf	/app/data/pr_computation/y6/6y6m/6y6m.pr.out
profile	/app/data/saxs_computation/y6/6y6m/6y6m.dat

solution structure of cold-shock domain 1 and 2 of drosophila Upstream of N-Ras (Unr)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Upstream of N-ras, isoform A

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)