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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P40089 New Search
14PDB entries
20Biological assembly
21chain/assembly records
Main Difference Dimensions in This Set
Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
3JCM Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP Deposited 2015-12-23 Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 34-meric（34） Consistent with all polymers
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
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 Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric（8） Consistent with all polymers
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 Assembly 2 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric（8） Consistent with all polymers
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 Assembly 3 Protein–RNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers
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 Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric（8） Consistent with all polymers
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 Assembly 2 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric（8） Consistent with all polymers
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 Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric（35） Consistent with all polymers
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 Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric（58） Consistent with all polymers
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 Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric（9） Consistent with all polymers
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 Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric（57） Consistent with all polymers
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 Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 60-meric（60） Consistent with all polymers
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
6ASO Structure of yeast U6 snRNP with 3'-phosphate terminated U6 RNA Deposited 2017-08-25 Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric（9） Consistent with all polymers
Chain E 1–93（93 aa）
Not recorded K POTASSIUM ION × 2 MN MANGANESE (II) ION × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；280 mM sodium potassium tartrate 22.5 % glycerol 17.5 % PEG 3,350 1 mM manganese chloride
Resolution 2.71 Å R-free 0.247

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.