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6aso

Structure of yeast U6 snRNP with 3'-phosphate terminated U6 RNA

Method: X-RAY DIFFRACTION Dmax: 110.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

U4/U6 snRNA-associated-splicing factor PRP24

Saccharomyces cerevisiae

UniProt P49960

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 Heteromer Protein × 8 RNA 1 PDB declaration: nonameric（9） Consistent with all polymer counts Chain A； UniProt 28–444 Not recorded U6 snRNA-associated Sm-like protein LSm2 × 1 （P38203） U6 snRNA-associated Sm-like protein LSm3 × 1 （P57743） U6 snRNA-associated Sm-like protein LSm4 × 1 （P40070） U6 snRNA-associated Sm-like protein LSm5 × 1 （P40089） U6 snRNA-associated Sm-like protein LSm6 × 1 （A6ZYX7） U6 snRNA-associated Sm-like protein LSm7 × 1 （P53905） U6 snRNA-associated Sm-like protein LSm8 × 1 （P47093） Saccharomyces cerevisiae strain HB_S_GIMBLETTROAD_9 chromosome XII sequence × 1 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

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 6ASO 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 ligand/ion 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 ligand/ion 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics 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
2KH9 Solution structure of yeast Prp24-RRM2 bound to a fragment of U6 RNA Deposited 2009-03-27 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 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 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 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 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 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 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 ligand/ion 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

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 2–418； UniProt 28–444

U6 snRNA-associated Sm-like protein LSm2

Saccharomyces cerevisiae

UniProt P38203

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 Heteromer Protein × 8 RNA 1 PDB declaration: nonameric（9） Consistent with all polymer counts Chain B； UniProt 1–95 Not recorded U4/U6 snRNA-associated-splicing factor PRP24 × 1 （P49960） U6 snRNA-associated Sm-like protein LSm3 × 1 （P57743） U6 snRNA-associated Sm-like protein LSm4 × 1 （P40070） U6 snRNA-associated Sm-like protein LSm5 × 1 （P40089） U6 snRNA-associated Sm-like protein LSm6 × 1 （A6ZYX7） U6 snRNA-associated Sm-like protein LSm7 × 1 （P53905） U6 snRNA-associated Sm-like protein LSm8 × 1 （P47093） Saccharomyces cerevisiae strain HB_S_GIMBLETTROAD_9 chromosome XII sequence × 1 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

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 6ASO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3JCM Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP Deposited 2015-12-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 34-meric
Chain c 1–95（95 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 M7M N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate) × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
4C8Q Crystal structure of the yeast Lsm1-7-Pat1 complex Deposited 2013-10-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 2–95（94 aa） Fragment：RESIDUES 2-95
Not recorded CO COBALT (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 100 MM HEPES PH 7.0, 20% MPD, 10 MM HEXAMINE COBALT(III) CHLORIDE
Resolution 3.70 Å R-free 0.295
4C92 Crystal structure of the yeast Lsm1-7 complex Deposited 2013-10-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 2–95（94 aa） Fragment：RESIDUES 2-95
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 100 MM MES PH 6.0, 40% MPD
Resolution 2.30 Å R-free 0.259
4M75 Crystal structure of Lsm1-7 complex Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 1–95（95 aa）
Mutation：C45S Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM MES 6.5, 25% PEG600, 20mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.291
4M75 Crystal structure of Lsm1-7 complex Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain I 1–95（95 aa）
Mutation：C45S 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；pH 6.5；291 K；100mM MES 6.5, 25% PEG600, 20mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.291
4M77 Crystal structure of Lsm2-8 complex, space group I212121 Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 1–95（95 aa）
Mutation：C45S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；20% PEG2000MME, 100mM Sodium Citrate 5.2, 10% 2-propanol, 50mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.11 Å R-free 0.267
4M77 Crystal structure of Lsm2-8 complex, space group I212121 Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain I 1–95（95 aa）
Mutation：C45S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；20% PEG2000MME, 100mM Sodium Citrate 5.2, 10% 2-propanol, 50mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.11 Å R-free 0.267
4M78 Crystal structure of Lsm2-8 complex, space group P21 Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 1–95（95 aa）
Mutation：C45S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 20mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.79 Å R-free 0.294
4M78 Crystal structure of Lsm2-8 complex, space group P21 Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain I 1–95（95 aa）
Mutation：C45S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 20mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.79 Å R-free 0.294
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain I 1–95（95 aa）
Mutation：C45S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain B 1–95（95 aa）
Mutation：C45S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–RNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain B 1–95（95 aa）
Chain I 1–95（95 aa）
Mutation：C45S Mutation：C45S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7D Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain B 1–95（95 aa）
Mutation：C45S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM Sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.283
4M7D Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain I 1–95（95 aa）
Mutation：C45S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM Sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.283
4N0A Crystal structure of Lsm2-3-Pat1C complex from Saccharomyces cerevisiae Deposited 2013-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain C 1–95（95 aa）
Chain D 1–95（95 aa）
Chain G 1–95（95 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；0.1M Tris, 12% ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 3.15 Å R-free 0.300
5GAN The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom Deposited 2015-12-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain 2 1–95（95 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
Resolution 3.70 Å
5NRL Structure of a pre-catalytic spliceosome Deposited 2017-04-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric
Chain a 1–95（95 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；Buffer pH: HEPES, 7.9; EDTA, 8.0
cryo-EM vitrification conditions Cryogen ETHANE；Grids were glow-discharged for 15 s before deposition of 3 microliter sample (~1.5 mg mL-1), and subsequently incubated for 2-3.5 s before blotting and vitrification by plunging into liquid ethane with a Vitrobot Mark III (FEI) operated at 4 degrees Celsius and 100% humidity.
Resolution 7.20 Å
5VSU Structure of yeast U6 snRNP with 2'-phosphate terminated U6 RNA Deposited 2017-05-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric
Chain B 1–95（95 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
5ZWM Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.4~4.6 angstrom (tri-snRNP and U2 snRNP Part) Deposited 2018-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric
Chain q 1–95（95 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
5ZWO Cryo-EM structure of the yeast B complex at average resolution of 3.9 angstrom Deposited 2018-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 60-meric
Chain q 1–95（95 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

14 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LSM2_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–95； UniProt 1–95

U6 snRNA-associated Sm-like protein LSm3

Saccharomyces cerevisiae

UniProt P57743

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 Heteromer Protein × 8 RNA 1 PDB declaration: nonameric（9） Consistent with all polymer counts Chain C； UniProt 1–89 Not recorded U4/U6 snRNA-associated-splicing factor PRP24 × 1 （P49960） U6 snRNA-associated Sm-like protein LSm2 × 1 （P38203） U6 snRNA-associated Sm-like protein LSm4 × 1 （P40070） U6 snRNA-associated Sm-like protein LSm5 × 1 （P40089） U6 snRNA-associated Sm-like protein LSm6 × 1 （A6ZYX7） U6 snRNA-associated Sm-like protein LSm7 × 1 （P53905） U6 snRNA-associated Sm-like protein LSm8 × 1 （P47093） Saccharomyces cerevisiae strain HB_S_GIMBLETTROAD_9 chromosome XII sequence × 1 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

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 6ASO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3BW1 Crystal structure of homomeric yeast Lsm3 exhibiting novel octameric ring organisation Deposited 2008-01-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–89（89 aa）
Chain B 1–89（89 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 16 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.75M lithium sulfate, 8% (v/v) 2-methyl-2,4-pentanediol, 0.1M imidazole (pH 7.0), 10mM uridine-5-monophosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.243
3JCM Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP Deposited 2015-12-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 34-meric
Chain d 1–89（89 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 M7M N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate) × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
4C8Q Crystal structure of the yeast Lsm1-7-Pat1 complex Deposited 2013-10-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–89（89 aa） Fragment：RESIDUES 1-89
Not recorded CO COBALT (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 100 MM HEPES PH 7.0, 20% MPD, 10 MM HEXAMINE COBALT(III) CHLORIDE
Resolution 3.70 Å R-free 0.295
4C92 Crystal structure of the yeast Lsm1-7 complex Deposited 2013-10-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–89（89 aa） Fragment：RESIDUES 1-89
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 100 MM MES PH 6.0, 40% MPD
Resolution 2.30 Å R-free 0.259
4M75 Crystal structure of Lsm1-7 complex Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–89（89 aa）
Mutation：C37S,C63S Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM MES 6.5, 25% PEG600, 20mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.291
4M75 Crystal structure of Lsm1-7 complex Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain J 1–89（89 aa）
Mutation：C37S,C63S 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；pH 6.5；291 K；100mM MES 6.5, 25% PEG600, 20mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.291
4M77 Crystal structure of Lsm2-8 complex, space group I212121 Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–89（89 aa）
Mutation：C37S,C63S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；20% PEG2000MME, 100mM Sodium Citrate 5.2, 10% 2-propanol, 50mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.11 Å R-free 0.267
4M77 Crystal structure of Lsm2-8 complex, space group I212121 Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain J 1–89（89 aa）
Mutation：C37S,C63S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；20% PEG2000MME, 100mM Sodium Citrate 5.2, 10% 2-propanol, 50mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.11 Å R-free 0.267
4M78 Crystal structure of Lsm2-8 complex, space group P21 Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–89（89 aa）
Mutation：C37S,C63S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 20mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.79 Å R-free 0.294
4M78 Crystal structure of Lsm2-8 complex, space group P21 Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain J 1–89（89 aa）
Mutation：C37S,C63S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 20mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.79 Å R-free 0.294
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain J 1–89（89 aa）
Mutation：C37S,C63S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain C 1–89（89 aa）
Mutation：C37S,C63S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–RNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–89（89 aa）
Chain J 1–89（89 aa）
Mutation：C37S,C63S Mutation：C37S,C63S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7D Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain C 1–89（89 aa）
Mutation：C37S,C63S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM Sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.283
4M7D Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain J 1–89（89 aa）
Mutation：C37S,C63S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM Sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.283
4N0A Crystal structure of Lsm2-3-Pat1C complex from Saccharomyces cerevisiae Deposited 2013-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain A 1–89（89 aa）
Chain B 1–89（89 aa）
Chain E 1–89（89 aa）
Chain F 1–89（89 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；0.1M Tris, 12% ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 3.15 Å R-free 0.300
5GAN The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom Deposited 2015-12-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain 3 1–89（89 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
Resolution 3.70 Å
5NRL Structure of a pre-catalytic spliceosome Deposited 2017-04-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric
Chain 3 1–89（89 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；Buffer pH: HEPES, 7.9; EDTA, 8.0
cryo-EM vitrification conditions Cryogen ETHANE；Grids were glow-discharged for 15 s before deposition of 3 microliter sample (~1.5 mg mL-1), and subsequently incubated for 2-3.5 s before blotting and vitrification by plunging into liquid ethane with a Vitrobot Mark III (FEI) operated at 4 degrees Celsius and 100% humidity.
Resolution 7.20 Å
5VSU Structure of yeast U6 snRNP with 2'-phosphate terminated U6 RNA Deposited 2017-05-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric
Chain C 1–89（89 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
5ZWM Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.4~4.6 angstrom (tri-snRNP and U2 snRNP Part) Deposited 2018-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric
Chain r 1–89（89 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
5ZWO Cryo-EM structure of the yeast B complex at average resolution of 3.9 angstrom Deposited 2018-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 60-meric
Chain r 1–89（89 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

15 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LSM3_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–89； UniProt 1–89

U6 snRNA-associated Sm-like protein LSm4

Saccharomyces cerevisiae

UniProt P40070

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 Heteromer Protein × 8 RNA 1 PDB declaration: nonameric（9） Consistent with all polymer counts Chain D； UniProt 1–93 Not recorded U4/U6 snRNA-associated-splicing factor PRP24 × 1 （P49960） U6 snRNA-associated Sm-like protein LSm2 × 1 （P38203） U6 snRNA-associated Sm-like protein LSm3 × 1 （P57743） U6 snRNA-associated Sm-like protein LSm5 × 1 （P40089） U6 snRNA-associated Sm-like protein LSm6 × 1 （A6ZYX7） U6 snRNA-associated Sm-like protein LSm7 × 1 （P53905） U6 snRNA-associated Sm-like protein LSm8 × 1 （P47093） Saccharomyces cerevisiae strain HB_S_GIMBLETTROAD_9 chromosome XII sequence × 1 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

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 6ASO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3JCM Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP Deposited 2015-12-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 34-meric
Chain h 1–187（187 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 M7M N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate) × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
4C8Q Crystal structure of the yeast Lsm1-7-Pat1 complex Deposited 2013-10-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–114（114 aa） Fragment：RESIDUES 1-114
Not recorded CO COBALT (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 100 MM HEPES PH 7.0, 20% MPD, 10 MM HEXAMINE COBALT(III) CHLORIDE
Resolution 3.70 Å R-free 0.295
4C92 Crystal structure of the yeast Lsm1-7 complex Deposited 2013-10-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 1–114（114 aa） Fragment：RESIDUES 1-114
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 100 MM MES PH 6.0, 40% MPD
Resolution 2.30 Å R-free 0.259
4M75 Crystal structure of Lsm1-7 complex Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain G 1–93（93 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM MES 6.5, 25% PEG600, 20mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.291
4M75 Crystal structure of Lsm1-7 complex Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain N 1–93（93 aa）
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；pH 6.5；291 K；100mM MES 6.5, 25% PEG600, 20mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.291
4M77 Crystal structure of Lsm2-8 complex, space group I212121 Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain G 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；20% PEG2000MME, 100mM Sodium Citrate 5.2, 10% 2-propanol, 50mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.11 Å R-free 0.267
4M77 Crystal structure of Lsm2-8 complex, space group I212121 Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain N 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；20% PEG2000MME, 100mM Sodium Citrate 5.2, 10% 2-propanol, 50mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.11 Å R-free 0.267
4M78 Crystal structure of Lsm2-8 complex, space group P21 Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain G 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 20mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.79 Å R-free 0.294
4M78 Crystal structure of Lsm2-8 complex, space group P21 Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain N 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 20mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.79 Å R-free 0.294
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain N 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain G 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–RNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain G 1–93（93 aa）
Chain N 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7D Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain G 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM Sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.283
4M7D Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain N 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM Sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.283
5GAN The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain 4 1–187（187 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
Resolution 3.70 Å
5NRL Structure of a pre-catalytic spliceosome Deposited 2017-04-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric
Chain j 1–187（187 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；Buffer pH: HEPES, 7.9; EDTA, 8.0
cryo-EM vitrification conditions Cryogen ETHANE；Grids were glow-discharged for 15 s before deposition of 3 microliter sample (~1.5 mg mL-1), and subsequently incubated for 2-3.5 s before blotting and vitrification by plunging into liquid ethane with a Vitrobot Mark III (FEI) operated at 4 degrees Celsius and 100% humidity.
Resolution 7.20 Å
5VSU Structure of yeast U6 snRNP with 2'-phosphate terminated U6 RNA Deposited 2017-05-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric
Chain D 1–93（93 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
5ZWM Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.4~4.6 angstrom (tri-snRNP and U2 snRNP Part) Deposited 2018-05-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric
Chain s 1–187（187 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
5ZWO Cryo-EM structure of the yeast B complex at average resolution of 3.9 angstrom Deposited 2018-05-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 60-meric
Chain s 1–187（187 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

13 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LSM4_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–93； UniProt 1–93

U6 snRNA-associated Sm-like protein LSm5

Saccharomyces cerevisiae

UniProt P40089

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 Heteromer Protein × 8 RNA 1 PDB declaration: nonameric（9） Consistent with all polymer counts Chain E； UniProt 1–93 Not recorded U4/U6 snRNA-associated-splicing factor PRP24 × 1 （P49960） U6 snRNA-associated Sm-like protein LSm2 × 1 （P38203） U6 snRNA-associated Sm-like protein LSm3 × 1 （P57743） U6 snRNA-associated Sm-like protein LSm4 × 1 （P40070） U6 snRNA-associated Sm-like protein LSm6 × 1 （A6ZYX7） U6 snRNA-associated Sm-like protein LSm7 × 1 （P53905） U6 snRNA-associated Sm-like protein LSm8 × 1 （P47093） Saccharomyces cerevisiae strain HB_S_GIMBLETTROAD_9 chromosome XII sequence × 1 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

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 6ASO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3JCM Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP Deposited 2015-12-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 34-meric
Chain f 1–93（93 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 M7M N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate) × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
4C8Q Crystal structure of the yeast Lsm1-7-Pat1 complex Deposited 2013-10-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–93（93 aa） Fragment：RESIDUES 1-93
Not recorded CO COBALT (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 100 MM HEPES PH 7.0, 20% MPD, 10 MM HEXAMINE COBALT(III) CHLORIDE
Resolution 3.70 Å R-free 0.295
4C92 Crystal structure of the yeast Lsm1-7 complex Deposited 2013-10-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 1–93（93 aa） Fragment：RESIDUES 1-93
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 100 MM MES PH 6.0, 40% MPD
Resolution 2.30 Å R-free 0.259
4M75 Crystal structure of Lsm1-7 complex Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 1–93（93 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM MES 6.5, 25% PEG600, 20mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.291
4M75 Crystal structure of Lsm1-7 complex Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain L 1–93（93 aa）
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；pH 6.5；291 K；100mM MES 6.5, 25% PEG600, 20mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.291
4M77 Crystal structure of Lsm2-8 complex, space group I212121 Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；20% PEG2000MME, 100mM Sodium Citrate 5.2, 10% 2-propanol, 50mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.11 Å R-free 0.267
4M77 Crystal structure of Lsm2-8 complex, space group I212121 Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain L 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；20% PEG2000MME, 100mM Sodium Citrate 5.2, 10% 2-propanol, 50mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.11 Å R-free 0.267
4M78 Crystal structure of Lsm2-8 complex, space group P21 Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 20mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.79 Å R-free 0.294
4M78 Crystal structure of Lsm2-8 complex, space group P21 Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain L 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 20mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.79 Å R-free 0.294
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain L 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain E 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–RNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain E 1–93（93 aa）
Chain L 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7D Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain E 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM Sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.283
4M7D Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain L 1–93（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM Sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.283
5GAN The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom Deposited 2015-12-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain 5 1–93（93 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
Resolution 3.70 Å
5NRL Structure of a pre-catalytic spliceosome Deposited 2017-04-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric
Chain o 1–93（93 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；Buffer pH: HEPES, 7.9; EDTA, 8.0
cryo-EM vitrification conditions Cryogen ETHANE；Grids were glow-discharged for 15 s before deposition of 3 microliter sample (~1.5 mg mL-1), and subsequently incubated for 2-3.5 s before blotting and vitrification by plunging into liquid ethane with a Vitrobot Mark III (FEI) operated at 4 degrees Celsius and 100% humidity.
Resolution 7.20 Å
5VSU Structure of yeast U6 snRNP with 2'-phosphate terminated U6 RNA Deposited 2017-05-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric
Chain E 1–93（93 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
5ZWM Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.4~4.6 angstrom (tri-snRNP and U2 snRNP Part) Deposited 2018-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric
Chain t 1–93（93 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
5ZWO Cryo-EM structure of the yeast B complex at average resolution of 3.9 angstrom Deposited 2018-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 60-meric
Chain t 1–93（93 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

13 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LSM5_YEAST
Isoform —
PDB entities 5
Chains and sequence ranges Author chain E； PDBConstruct 1–93； UniProt 1–93

U6 snRNA-associated Sm-like protein LSm6

Saccharomyces cerevisiae

UniProt A6ZYX7

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 Heteromer Protein × 8 RNA 1 PDB declaration: nonameric（9） Consistent with all polymer counts Chain F； UniProt 1–86 Not recorded U4/U6 snRNA-associated-splicing factor PRP24 × 1 （P49960） U6 snRNA-associated Sm-like protein LSm2 × 1 （P38203） U6 snRNA-associated Sm-like protein LSm3 × 1 （P57743） U6 snRNA-associated Sm-like protein LSm4 × 1 （P40070） U6 snRNA-associated Sm-like protein LSm5 × 1 （P40089） U6 snRNA-associated Sm-like protein LSm7 × 1 （P53905） U6 snRNA-associated Sm-like protein LSm8 × 1 （P47093） Saccharomyces cerevisiae strain HB_S_GIMBLETTROAD_9 chromosome XII sequence × 1 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

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 6ASO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5GAN The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom Deposited 2015-12-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain 6 1–86（86 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
Resolution 3.70 Å
5NRL Structure of a pre-catalytic spliceosome Deposited 2017-04-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric
Chain z 1–86（86 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；Buffer pH: HEPES, 7.9; EDTA, 8.0
cryo-EM vitrification conditions Cryogen ETHANE；Grids were glow-discharged for 15 s before deposition of 3 microliter sample (~1.5 mg mL-1), and subsequently incubated for 2-3.5 s before blotting and vitrification by plunging into liquid ethane with a Vitrobot Mark III (FEI) operated at 4 degrees Celsius and 100% humidity.
Resolution 7.20 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LSM6_YEAS7
Isoform —
PDB entities 6
Chains and sequence ranges Author chain F； PDBConstruct 3–88； UniProt 1–86

U6 snRNA-associated Sm-like protein LSm7

Saccharomyces cerevisiae

UniProt P53905

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 Heteromer Protein × 8 RNA 1 PDB declaration: nonameric（9） Consistent with all polymer counts Chain G； UniProt 1–115 Not recorded U4/U6 snRNA-associated-splicing factor PRP24 × 1 （P49960） U6 snRNA-associated Sm-like protein LSm2 × 1 （P38203） U6 snRNA-associated Sm-like protein LSm3 × 1 （P57743） U6 snRNA-associated Sm-like protein LSm4 × 1 （P40070） U6 snRNA-associated Sm-like protein LSm5 × 1 （P40089） U6 snRNA-associated Sm-like protein LSm6 × 1 （A6ZYX7） U6 snRNA-associated Sm-like protein LSm8 × 1 （P47093） Saccharomyces cerevisiae strain HB_S_GIMBLETTROAD_9 chromosome XII sequence × 1 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

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 6ASO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3JCM Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP Deposited 2015-12-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 34-meric
Chain g 1–115（115 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 M7M N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate) × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
4C8Q Crystal structure of the yeast Lsm1-7-Pat1 complex Deposited 2013-10-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 1–115（115 aa） Fragment：RESIDUES 1-115
Not recorded CO COBALT (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 100 MM HEPES PH 7.0, 20% MPD, 10 MM HEXAMINE COBALT(III) CHLORIDE
Resolution 3.70 Å R-free 0.295
4C92 Crystal structure of the yeast Lsm1-7 complex Deposited 2013-10-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain G 1–115（115 aa） Fragment：RESIDUES 1-115
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 100 MM MES PH 6.0, 40% MPD
Resolution 2.30 Å R-free 0.259
4M75 Crystal structure of Lsm1-7 complex Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–115（115 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM MES 6.5, 25% PEG600, 20mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.291
4M75 Crystal structure of Lsm1-7 complex Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain M 1–115（115 aa）
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；pH 6.5；291 K；100mM MES 6.5, 25% PEG600, 20mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.291
4M77 Crystal structure of Lsm2-8 complex, space group I212121 Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–115（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；20% PEG2000MME, 100mM Sodium Citrate 5.2, 10% 2-propanol, 50mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.11 Å R-free 0.267
4M77 Crystal structure of Lsm2-8 complex, space group I212121 Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain M 1–115（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；20% PEG2000MME, 100mM Sodium Citrate 5.2, 10% 2-propanol, 50mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.11 Å R-free 0.267
4M78 Crystal structure of Lsm2-8 complex, space group P21 Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–115（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 20mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.79 Å R-free 0.294
4M78 Crystal structure of Lsm2-8 complex, space group P21 Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain M 1–115（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 20mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.79 Å R-free 0.294
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain M 1–115（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain F 1–115（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–RNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain F 1–115（115 aa）
Chain M 1–115（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7D Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain F 1–115（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM Sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.283
4M7D Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU Deposited 2013-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain M 1–115（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM Sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.283
5GAN The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom Deposited 2015-12-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain 7 1–115（115 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
Resolution 3.70 Å
5NRL Structure of a pre-catalytic spliceosome Deposited 2017-04-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric
Chain 7 1–115（115 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；Buffer pH: HEPES, 7.9; EDTA, 8.0
cryo-EM vitrification conditions Cryogen ETHANE；Grids were glow-discharged for 15 s before deposition of 3 microliter sample (~1.5 mg mL-1), and subsequently incubated for 2-3.5 s before blotting and vitrification by plunging into liquid ethane with a Vitrobot Mark III (FEI) operated at 4 degrees Celsius and 100% humidity.
Resolution 7.20 Å
5VSU Structure of yeast U6 snRNP with 2'-phosphate terminated U6 RNA Deposited 2017-05-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric
Chain G 1–115（115 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
5ZWM Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.4~4.6 angstrom (tri-snRNP and U2 snRNP Part) Deposited 2018-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric
Chain y 1–115（115 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
5ZWO Cryo-EM structure of the yeast B complex at average resolution of 3.9 angstrom Deposited 2018-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 60-meric
Chain y 1–115（115 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

13 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LSM7_YEAST
Isoform —
PDB entities 7
Chains and sequence ranges Author chain G； PDBConstruct 1–115； UniProt 1–115

U6 snRNA-associated Sm-like protein LSm8

Saccharomyces cerevisiae

UniProt P47093

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 Heteromer Protein × 8 RNA 1 PDB declaration: nonameric（9） Consistent with all polymer counts Chain H； UniProt 1–109 Not recorded U4/U6 snRNA-associated-splicing factor PRP24 × 1 （P49960） U6 snRNA-associated Sm-like protein LSm2 × 1 （P38203） U6 snRNA-associated Sm-like protein LSm3 × 1 （P57743） U6 snRNA-associated Sm-like protein LSm4 × 1 （P40070） U6 snRNA-associated Sm-like protein LSm5 × 1 （P40089） U6 snRNA-associated Sm-like protein LSm6 × 1 （A6ZYX7） U6 snRNA-associated Sm-like protein LSm7 × 1 （P53905） Saccharomyces cerevisiae strain HB_S_GIMBLETTROAD_9 chromosome XII sequence × 1 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

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 6ASO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3JCM Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP Deposited 2015-12-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 34-meric
Chain b 1–109（109 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 M7M N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate) × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
4M77 Crystal structure of Lsm2-8 complex, space group I212121 Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 1–109（109 aa）
Mutation：K17L,C22S,I38L,C51S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；20% PEG2000MME, 100mM Sodium Citrate 5.2, 10% 2-propanol, 50mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.11 Å R-free 0.267
4M77 Crystal structure of Lsm2-8 complex, space group I212121 Deposited 2013-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain H 1–109（109 aa）
Mutation：K17L,C22S,I38L,C51S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；20% PEG2000MME, 100mM Sodium Citrate 5.2, 10% 2-propanol, 50mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.11 Å R-free 0.267
4M78 Crystal structure of Lsm2-8 complex, space group P21 Deposited 2013-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 1–96（96 aa）
Mutation：K17L,C22S,I38L,C51S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 20mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.79 Å R-free 0.294
4M78 Crystal structure of Lsm2-8 complex, space group P21 Deposited 2013-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain H 1–96（96 aa）
Mutation：K17L,C22S,I38L,C51S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 20mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.79 Å R-free 0.294
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain H 1–96（96 aa）
Mutation：K17L,C22S,I38L,C51S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain A 1–96（96 aa）
Mutation：K17L,C22S,I38L,C51S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7A Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA Deposited 2013-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–RNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain A 1–96（96 aa）
Chain H 1–96（96 aa）
Mutation：K17L,C22S,I38L,C51S Mutation：K17L,C22S,I38L,C51S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.78 Å R-free 0.278
4M7D Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU Deposited 2013-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain A 1–96（96 aa）
Mutation：K17L,C22S,I38L,C51S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM Sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.283
4M7D Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU Deposited 2013-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric
Chain H 1–96（96 aa）
Mutation：K17L,C22S,I38L,C51S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100mM Sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.283
5GAN The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom Deposited 2015-12-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain 8 1–109（109 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
Resolution 3.70 Å
5NRL Structure of a pre-catalytic spliceosome Deposited 2017-04-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric
Chain 8 1–109（109 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；Buffer pH: HEPES, 7.9; EDTA, 8.0
cryo-EM vitrification conditions Cryogen ETHANE；Grids were glow-discharged for 15 s before deposition of 3 microliter sample (~1.5 mg mL-1), and subsequently incubated for 2-3.5 s before blotting and vitrification by plunging into liquid ethane with a Vitrobot Mark III (FEI) operated at 4 degrees Celsius and 100% humidity.
Resolution 7.20 Å
5VSU Structure of yeast U6 snRNP with 2'-phosphate terminated U6 RNA Deposited 2017-05-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric
Chain H 1–109（109 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
5ZWM Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.4~4.6 angstrom (tri-snRNP and U2 snRNP Part) Deposited 2018-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric
Chain z 1–109（109 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
5ZWO Cryo-EM structure of the yeast B complex at average resolution of 3.9 angstrom Deposited 2018-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 60-meric
Chain z 1–109（109 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

10 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LSM8_YEAST
Isoform —
PDB entities 8
Chains and sequence ranges Author chain H； PDBConstruct 1–109； UniProt 1–109

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6aso

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6aso
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6aso
Deposition date deposition_date2017-08-25
Structure title titleStructure of yeast U6 snRNP with 3'-phosphate terminated U6 RNA
Keywords keywordsLsm2-8 spliceosome U6 Prp24, SPLICING; SPLICING
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.18 Å
Radius of gyration Rg (electron density) rg_electron34.92 Å
Forward intensity I(0) i0302869000.00
Molecular weight molecular_weight125640.0 kDa
Excluded volume excluded_volume151150 ų
Envelope volume envelope_volume210760 ų
Hydration-shell volume shell_volume50069 ų
Envelope diameter envelope_diameter114.2 Å
Shell Rg shell_rg41.92 Å
Envelope Rg envelope_rg34.00 Å
Shape Rg shape_rg34.94 Å
Total Rg total_rg35.31 Å
Total atoms total_atoms8723
Residues n_residues975
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax110.8 Å
Rg (real space) rg_real35.03 Å
Rg uncertainty (real space) rg_real_error0.60 Å
I(0) (real space) i0_real3.0290e+08
I(0) uncertainty (real space) i0_real_error4.4440e+06
Rg (reciprocal space) rg_reciprocal35.13 Å
I(0) (reciprocal space) i0_reciprocal302900000.0000
Solution quality estimate total_estimate0.9040
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.3 Å
Skewness Skewness skewness0.154
Kurtosis Kurtosis kurtosis-0.534
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha22420000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.935
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (13)

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7. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

Domain ID domain_id6asoA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
Domain ID domain_id6asoA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
Domain ID domain_id6asoA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
Domain ID domain_id6asoA04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
Domain ID domain_id6asoB00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily100 —
Domain ID domain_id6asoC00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily100 —
Domain ID domain_id6asoD00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily100 —
Domain ID domain_id6asoE00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily100 —
Domain ID domain_id6asoF00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily100 —
Domain ID domain_id6asoG00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily100 —
Domain ID domain_id6asoH00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily100 —
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8. Citations (1)

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9. Files and Curves (10)