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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 38–197 | Fragment：(RRM domains 1 and 2) | No other associated polymer | 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 |
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 2GO9 | 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 |
| 2KH9 Solution structure of yeast Prp24-RRM2 bound to a fragment of U6 RNA Deposited 2009-03-27 | Different construct Different oligomeric state Different experimental conditions | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
115–197（83 aa）
Fragment：UNP residues 115-197
|
Not recorded | No recorded non-water small molecule |
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 |
| 2L9W Solution Structure of the C-terminal domain of Prp24 Deposited 2011-02-25 | Different construct 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 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
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 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
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 oligomeric state 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 2–161； UniProt 38–197 |
