SAXSdb — 2kh9

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

U4/U6 snRNA-associated-splicing factor PRP24

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–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 115–197	Fragment：UNP residues 115-197	5'-R(APGPAPGPAPU)-3' × 1	SOLUTION NMR NMR measurement conditions：pH 7；298.15 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition：300 uM Prp24-RRM2-1, 3 mM AGAGAU-2, 10 mM [U-2H] TRIS-3, 50 mM potassium chloride-4, 100% D2O \| 100% D2O NMR sample composition：500 uM [U-99% 15N] Prp24-RRM2-5, 5 mM AGAGAU-6, 10 mM [U-2H] TRIS-7, 50 mM potassium chloride-8, 100% D2O \| 100% D2O NMR sample composition：500 mM [U-99% 13C; U-99% 15N] Prp24-RRM2-9, 5 mM AGAGAU-10, 10 mM TRIS-11, 50 mM potassium chloride-12, 1 mM DTT-13, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：500 uM [U-99% 13C; U-99% 15N] Prp24-RRM2-14, 5 mM AGAGAU-15, 10 mM TRIS-16, 50 mM potassium chloride-17, 1 mM DTT-18, 10 uM DSS-19, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：300 uM [U-99% 13C; U-99% 15N] Prp24-RRM2-20, 3 mM AGAGAU-21, 10 mM TRIS-22, 50 mM potassium chloride-23, 1 mM DTT-24, 6.5 % DMPC/DHPC 3:1-25, 90% H2O/10% D2O \| 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 2KH9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2GHP Crystal structure of the N-terminal 3 RNA binding domains of the yeast splicing factor Prp24 Deposited 2006-03-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–291（291 aa） Chain B 1–291（291 aa） Chain C 1–291（291 aa） Chain D 1–291（291 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.0003 M TCEP, 0.005 TRIS PH 8.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (14% MEPEG 5000, 0.20 M TETRAMETHYL AMMONIUM CHLORIDE, 0.10 M SODIUM SUCCINATE PH 4.0) Crystals cryo-protected with the well solution supplemented with 30% ethylene glycol., VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.264
2GHP Crystal structure of the N-terminal 3 RNA binding domains of the yeast splicing factor Prp24 Deposited 2006-03-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–291（291 aa） Chain F 1–291（291 aa） Chain G 1–291（291 aa） Chain H 1–291（291 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.0003 M TCEP, 0.005 TRIS PH 8.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (14% MEPEG 5000, 0.20 M TETRAMETHYL AMMONIUM CHLORIDE, 0.10 M SODIUM SUCCINATE PH 4.0) Crystals cryo-protected with the well solution supplemented with 30% ethylene glycol., VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.264
2GO9 RRM domains 1 and 2 of Prp24 from S. cerevisiae Deposited 2006-04-12	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 38–197（160 aa） Fragment：(RRM domains 1 and 2)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.1 M KCl；Pressure AMBIENT NMR sample composition 0.3-0.8 mM protein, 50 mM K(PO)4 (pH 6.5), 100 mM KCl, 2 mM DTT \| 90% H2O/10% D2O	Resolution not provided
2L9W Solution Structure of the C-terminal domain of Prp24 Deposited 2011-02-25	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 292–400（109 aa） Fragment：C-terminal residues 292-400	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Pressure ambient NMR measurement conditions pH 6；304 K；Pressure ambient NMR sample composition 600 uM [U-99% 13C; U-99% 15N] L4W, 18 mM potassium phosphate pH 6, 45 mM potassium chloride, 0.9 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 600 uM [U-99% 13C; U-99% 15N] L4W, 18 mM [U-99% 2H] potassium phosphate pH 6, 45 mM [U-99% 2H] potassium chloride, 100% D2O \| 100% D2O NMR sample composition 600 uM [U-99% 13C; U-99% 15N] L4W, 18 mM potassium phosphate pH 6, 45 mM potassium chloride, 1 uM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 600 uM L4W, 18 mM [U-99% 2H] potassium phosphate pH 6, 45 mM [U-99% 2H] potassium chloride, 100% D2O \| 100% D2O NMR sample composition 600 uM [U-99% 13C; U-99% 15N] L4W, 18 mM potassium phosphate pH 6, 45 mM potassium chloride, 0.9 mM DTT, 6.5 % DMPC/DHPC q=3, 0.67 mg/mL CTAB, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4N0T Core structure of the U6 small nuclear ribonucleoprotein at 1.7 Angstrom resolution Deposited 2013-10-02	Different construct 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 34–400（367 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；274 K；100 mM lithium sulfate, 100 mM sodium citrate, pH 5.5, 20 % PEG 1,000, VAPOR DIFFUSION, SITTING DROP, temperature 274K	Resolution 1.70 Å R-free 0.211
5TF6 Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core Deposited 2016-09-24	Different construct 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 34–400（367 aa） Fragment：UNP residues 34-400	Not recorded	K POTASSIUM ION × 2 CL CHLORIDE ION × 2 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；1 M lithium chloride, 100 mM sodium MES, 64 mM hydrochloric acid, 25% PEG 8,000, 20% glycerol, 1 mM MnCl2, 400 mM potassium chloride, 10 mM HEPES acid, 10 mM Tris base, 2 mM MgCl2, 1 mM TCEP-HCl	Resolution 2.30 Å R-free 0.232
5TF6 Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core Deposited 2016-09-24	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain C 34–400（367 aa） Fragment：UNP residues 34-400	Not recorded	K POTASSIUM ION × 3 CL CHLORIDE ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；1 M lithium chloride, 100 mM sodium MES, 64 mM hydrochloric acid, 25% PEG 8,000, 20% glycerol, 1 mM MnCl2, 400 mM potassium chloride, 10 mM HEPES acid, 10 mM Tris base, 2 mM MgCl2, 1 mM TCEP-HCl	Resolution 2.30 Å R-free 0.232
5VSU Structure of yeast U6 snRNP with 2'-phosphate terminated U6 RNA Deposited 2017-05-12	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric	Chain A 1–444（444 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；289 K；0.2 M NH4F 0.1 M HEPES pH 7.4 0.01 M MgCl2 18 % PEG 3,350	Resolution 3.10 Å R-free 0.298
6ASO Structure of yeast U6 snRNP with 3'-phosphate terminated U6 RNA Deposited 2017-08-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric	Chain A 28–444（417 aa）	Not recorded	K POTASSIUM ION × 2 MN MANGANESE (II) ION × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；280 mM sodium potassium tartrate 22.5 % glycerol 17.5 % PEG 3,350 1 mM manganese chloride	Resolution 2.71 Å R-free 0.247

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRP24_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–84； UniProt 115–197

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	2kh9
Deposition date deposition_date	2009-03-27
Structure title title	Solution structure of yeast Prp24-RRM2 bound to a fragment of U6 RNA
Keywords keywords	Protein/RNA, RRM, snRNP, Splicing, mRNA processing, mRNA splicing, Nucleus, Phosphoprotein, RNA-binding, SPLICING-RNA COMPLEX; SPLICING/RNA
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	13.19 Å
Radius of gyration Rg (electron density) rg_electron	12.85 Å
Forward intensity I(0) i0	246596000.00
Molecular weight molecular_weight	119120.0 kDa
Excluded volume excluded_volume	143920 Å³
Envelope volume envelope_volume	22133 Å³
Hydration-shell volume shell_volume	13055 Å³
Envelope diameter envelope_diameter	48.3 Å
Shell Rg shell_rg	20.25 Å
Envelope Rg envelope_rg	14.66 Å
Shape Rg shape_rg	12.81 Å
Total Rg total_rg	13.18 Å
Total atoms total_atoms	16120
Residues n_residues	920
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	44.8 Å
Rg (real space) rg_real	13.08 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	2.4660e+08
I(0) uncertainty (real space) i0_real_error	2.6310e+06
Rg (reciprocal space) rg_reciprocal	13.09 Å
I(0) (reciprocal space) i0_reciprocal	246600000.0000
Solution quality estimate total_estimate	0.8641
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.7 Å
Skewness Skewness skewness	0.073
Kurtosis Kurtosis kurtosis	-0.355
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	244800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.748; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.984

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2kh9A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

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8. Citations (1)

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Description description	U4/U6 snRNA-associated-splicing factor PRP24
Molecular weight formula_weight	10841.4 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	16120

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

Description description	5'-R(APGPAPGPAPU)-3'
Molecular weight formula_weight	1939.2 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/kh/2kh9/2kh9.fit
pddf	/app/data/pr_computation/kh/2kh9/2kh9.pr.out
profile	/app/data/saxs_computation/kh/2kh9/2kh9.dat

Solution structure of yeast Prp24-RRM2 bound to a fragment of U6 RNA

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

U4/U6 snRNA-associated-splicing factor PRP24

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)