SAXSdb — 2aqa

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

H/ACA ribonucleoprotein complex subunit 3

Saccharomyces cerevisiae

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 2–58	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 5；298 K；Ionic strength (raw mmCIF value) 50mM; 100mM；Pressure 1 NMR sample composition：1mM yNop10p unlabelled; Sodium Acetate, KCl \| 90% H2O/10% D2O NMR sample composition：1mM yNop10p unlabelled; Sodium Acetate, KCl \| 100% D2O NMR sample composition：1mM yNop10p 15N-labelled; Sodium Acetate, KCl \| 90% H2O/10% D2O NMR sample composition：1mM yNop10p 15N,13C-labelled; Sodium Acetate, KCl \| 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 2AQA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Y2Y Structural Characterization of Nop10p using Nuclear Magnetic Resonance Spectroscopy Deposited 2004-11-23	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–58（58 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；288 K；Ionic strength (raw mmCIF value) 110 mM；Pressure ambient NMR sample composition 1.5 mM 15N/13C Nop1p0p; 10 mM potassium phosphate buffer, pH 6.5; 100 mM potassium chloride; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.5 mM 15N/13C Nop1p0p; 10 mM potassium phosphate buffer, pH 6.5; 100 mM potassium chloride; 100% D2O \| 100% D2O	Resolution not provided
3U28 Crystal structure of a Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae Deposited 2011-10-02	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–58（58 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.04；293 K；0.2M sodium malonate, 7%(w/v) polyethylene glycol 3350, pH 8.04, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.233
3UAI Structure of the Shq1-Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae Deposited 2011-10-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–58（58 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；297 K；0.1M Bis-Tris, 20%(w/v) polyethylene glycol monomethyl ether 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 3.06 Å R-free 0.275
9G25 snR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 Deposited 2024-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain B 1–58（58 aa） Chain F 1–58（58 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.89 Å
9G28 snR30 snoRNP - State 2 - Utp23-Krr1-deltaC3 Deposited 2024-07-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain B 1–58（58 aa） Chain F 1–58（58 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NOP10_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–57； UniProt 2–58

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	2aqa
Deposition date deposition_date	2005-08-17
Structure title title	NMR structural analysis of Nop10p from Saccharomyces cerevisiae
Keywords keywords	Nop10p, 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	38.75 Å
Radius of gyration Rg (electron density) rg_electron	39.19 Å
Forward intensity I(0) i0	243251000.00
Molecular weight molecular_weight	129890.0 kDa
Excluded volume excluded_volume	164230 Å³
Envelope volume envelope_volume	253940 Å³
Hydration-shell volume shell_volume	48687 Å³
Envelope diameter envelope_diameter	181.0 Å
Shell Rg shell_rg	45.25 Å
Envelope Rg envelope_rg	47.86 Å
Shape Rg shape_rg	39.23 Å
Total Rg total_rg	39.41 Å
Total atoms total_atoms	18680
Residues n_residues	1140
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	164.9 Å
Rg (real space) rg_real	39.29 Å
Rg uncertainty (real space) rg_real_error	3.19 Å
I(0) (real space) i0_real	2.4330e+08
I(0) uncertainty (real space) i0_real_error	5.2060e+06
Rg (reciprocal space) rg_reciprocal	38.96 Å
I(0) (reciprocal space) i0_reciprocal	243200000.0000
Solution quality estimate total_estimate	0.6024
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	56.3 Å
Skewness Skewness skewness	0.393
Kurtosis Kurtosis kurtosis	-0.250
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	691900.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.172; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.310; 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

SCOP 2.08 (1 domains)

Domain ID domain_id	d2aqaa1
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.16 — Nop10-like SnoRNP
Family Family family	g.41.16.1 — Nucleolar RNA-binding protein Nop10-like

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8. Citations (1)

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Description description	H/ACA ribonucleoprotein complex subunit 3
Molecular weight formula_weight	7347.4 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	18680

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/aq/2aqa/2aqa.fit
pddf	/app/data/pr_computation/aq/2aqa/2aqa.pr.out
profile	/app/data/saxs_computation/aq/2aqa/2aqa.dat

NMR structural analysis of Nop10p from Saccharomyces cerevisiae

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

H/ACA ribonucleoprotein complex subunit 3

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

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)