SAXSdb — 7zhh

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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–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 756–990	Not recorded	;RNA (5'-R(PAPAPAPAPAPA)-3') ; × 1 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

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 7ZHH	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 oligomeric state 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
6Y6E drosophila Unr CSD456 Deposited 2020-02-26	Different construct Different oligomeric state Different ligand/ion 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 oligomeric state 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 oligomeric state 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
7ZHR Complex structure of drosophila Unr CSD789 and pAbp RRM3 Deposited 2022-04-07	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 2–236； UniProt 756–990

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	7zhh
Deposition date deposition_date	2022-04-06
Structure title title	Complex structure of drosophila Unr CSD789 and a poly(A) RNA sequence
Keywords keywords	drosophila Unr, CSD, cold-shock domain, protein-RNA complex, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	20.51 Å
Radius of gyration Rg (electron density) rg_electron	19.64 Å
Forward intensity I(0) i0	13458100.00
Molecular weight molecular_weight	25878.0 kDa
Excluded volume excluded_volume	31697 Å³
Envelope volume envelope_volume	40199 Å³
Hydration-shell volume shell_volume	17677 Å³
Envelope diameter envelope_diameter	64.4 Å
Shell Rg shell_rg	25.08 Å
Envelope Rg envelope_rg	19.58 Å
Shape Rg shape_rg	19.64 Å
Total Rg total_rg	20.41 Å
Total atoms total_atoms	1815
Residues n_residues	225
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	63.0 Å
Rg (real space) rg_real	20.42 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	1.3460e+07
I(0) uncertainty (real space) i0_real_error	1.4890e+05
Rg (reciprocal space) rg_reciprocal	20.44 Å
I(0) (reciprocal space) i0_reciprocal	13460000.0000
Solution quality estimate total_estimate	0.9146
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.1 Å
Skewness Skewness skewness	0.128
Kurtosis Kurtosis kurtosis	-0.601
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2812000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Upstream of N-ras, isoform A
Molecular weight formula_weight	26166.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2097

GAGSDAGQVYRGFIAVMKENFGFIETLSHDEEVFFHFSNYMGNPNWLELGQEVEYTLARNGNTSVSGNCLPAENVRMLPKNSIPQPAVLETTHNGVVARPLRCINPDQQEYAGLIEILDELRTTVISQHEFGITSLVNKRDLLQKGDLVSFRIDESGRAACVNAVRQKKRATVDSIKGQFGFLNFEVEDGKKLFFHMSEVQGNTVALHPGDTVEFSVVTNQRNGKSSACNVLKIND

来源 Source

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;RNA (5'-R(PAPAPAPAPAPA)-3') ;
Molecular weight formula_weight	4893.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C

AAAAAAAAAAAAAAA

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	266

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7zhhA01
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

Domain ID domain_id	7zhhA02
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 (3)

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Unit-cell length a length_a	97.920 Å
Unit-cell length b length_b	36.780 Å
Unit-cell length c length_c	85.830 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.81 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	48.790 Å
R factor r_factor	0.1884
R_work r_work	0.1872
R_free r_free	0.2100

fit	/app/data/saxs_computation/zh/7zhh/7zhh.fit
pddf	/app/data/pr_computation/zh/7zhh/7zhh.pr.out
profile	/app/data/saxs_computation/zh/7zhh/7zhh.dat

Complex structure of drosophila Unr CSD789 and a poly(A) RNA sequence

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)