Human spliceosomal PM5 C* complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8c6j
Q-score: 0.353
Dybkov O, Preussner M, El Ayoubi L, Feng VY, Harnisch C, Merz K, Leupold P, Yudichev P, Agafonov DE, Will CL, Girard C, Dienemann C, Urlaub H, Kastner B, Heyd F, Luehrmann R
Sci Adv (2023) 9 pp. eadf1785- [ Pubmed: 36867703 DOI: doi:10.1126/sciadv.adf1785 ]
- Prkr-interacting protein 1 (21 kDa, Protein from Homo sapiens)
- U2 snrna (60 kDa, RNA from Homo sapiens)
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from Homo sapiens)
- Nf-kappa-b-activating protein (47 kDa, Protein from Homo sapiens)
- Peptidyl-prolyl cis-trans isomerase-like 3 (18 kDa, Protein from Homo sapiens)
- U5 small nuclear ribonucleoprotein 200 kda helicase (244 kDa, Protein from Homo sapiens)
- 116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from Homo sapiens)
- Splicing factor cactin (88 kDa, Protein from Homo sapiens)
- Intron-binding protein aquarius (171 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- U6 snrna (34 kDa, RNA from Homo sapiens)
- U2 small nuclear ribonucleoprotein b'' (25 kDa, Protein from Homo sapiens)
- U5 small nuclear ribonucleoprotein 40 kda protein (39 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor isy1 homolog (33 kDa, Protein from Homo sapiens)
- Peptidyl-prolyl cis-trans isomerase-like 1 (18 kDa, Protein from Homo sapiens)
- Protein mago nashi homolog (17 kDa, Protein from Homo sapiens)
- Protein bud31 homolog (17 kDa, Protein from Homo sapiens)
- Cell division cycle 5-like protein (92 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
- U5 snrna (36 kDa, RNA from Homo sapiens)
- Snw domain-containing protein 1 (61 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna-binding protein 8a (19 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor rbm22 (46 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor syf2 (28 kDa, Protein from Homo sapiens)
- Pm5 5' exon (78 kDa, RNA from Homo sapiens)
- Pre-mrna-processing factor 19 (55 kDa, Protein from Homo sapiens)
- Probable atp-dependent rna helicase ddx41 (69 kDa, Protein from Homo sapiens)
- Eukaryotic initiation factor 4a-iii (46 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor cwc22 homolog (57 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Homo sapiens)
- Nitric oxide synthase-interacting protein (33 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor slu7 (68 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Sting er exit protein (25 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor spf27 (26 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
- Pre-mrna-processing factor 17 (65 kDa, Protein from Homo sapiens)
- Splicing factor c9orf78 (33 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
- Peptidyl-prolyl cis-trans isomerase e (33 kDa, Protein from Homo sapiens)
- Protein fam32a (13 kDa, Protein from Homo sapiens)
- Atp-dependent rna helicase dhx8 (139 kDa, Protein from Homo sapiens)
- Pm5 intron (74 kDa, RNA from Homo sapiens)
- Protein fam50a (40 kDa, Protein from Homo sapiens)
- Pleiotropic regulator 1 (57 kDa, Protein from Homo sapiens)
- U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Homo sapiens)
- Inositol hexakisphosphate (660 Da, Ligand)
- Crooked neck-like protein 1 (83 kDa, Protein from Homo sapiens)
- Splicing factor ess-2 homolog (52 kDa, Protein from Homo sapiens)
- Splicing regulator sde2 (49 kDa, Protein from Homo sapiens)
- Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
- Serine/arginine repetitive matrix protein 2 (300 kDa, Protein from Homo sapiens)
- Human spliceosomal c* complex assembled on pm5 pre-mrna (Complex from Homo sapiens)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
Resolution: 8.0 Å
EM Method: Single-particle
Fitted PDBs: 7abi
Q-score: 0.145
Townsend C, Leelaram MN, Agafonov DE, Dybkov O, Will CL, Bertram K, Urlaub H, Kastner B, Stark H, Luhrmann R
Science (2020) 370 [ Pubmed: 33243851 DOI: doi:10.1126/science.abc3753 ]
- Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from Human)
- Serine/arginine repetitive matrix protein 1 (102 kDa, Protein from Human)
- Peptidyl-prolyl cis-trans isomerase e (33 kDa, Protein from Human)
- Ring-type e3 ubiquitin-protein ligase ppil2 (58 kDa, Protein from Human)
- Minx m3 pre-mrna (103 kDa, RNA from synthetic construct)
- Inositol hexakisphosphate (660 Da, Ligand)
- Splicing factor 3a subunit 1 (88 kDa, Protein from Human)
- Splicing factor 3b subunit 2 (100 kDa, Protein from Human)
- Human pre-bact-2 spliceosome (Complex)
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Human)
- Beta-catenin-like protein 1 (65 kDa, Protein from Human)
- Smad nuclear-interacting protein 1 (45 kDa, Protein from Human)
- Cell division cycle 5-like protein (92 kDa, Protein from Human)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Human)
- U5 snrna (36 kDa, RNA from Human)
- Splicing factor 3a subunit 3 (58 kDa, Protein from Human)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Human)
- Splicing factor 3b subunit 6 (14 kDa, Protein from Human)
- 116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from Human)
- Snw domain-containing protein 1 (61 kDa, Protein from Human)
- Dna/rna-binding protein kin17 (45 kDa, Protein from Human)
- Minx m3 pre-mrna (Complex from synthetic construct)
- Pre-mrna-processing factor 17 (65 kDa, Protein from Human)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Human)
- Microfibrillar-associated protein 1 (52 kDa, Protein from Human)
- Intron-binding protein aquarius (171 kDa, Protein from Human)
- Zinc finger matrin-type protein 2 (23 kDa, Protein from Human)
- Pre-mrna-splicing factor 38a (37 kDa, Protein from Human)
- Splicing factor 3b subunit 5 (10 kDa, Protein from Human)
- Pre-mrna-splicing factor rbm22 (46 kDa, Protein from Human)
- U2 snrna (60 kDa, RNA from Human)
- Splicing factor 3a subunit 2 (49 kDa, Protein from Human)
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from Human)
- Pleiotropic regulator 1 (57 kDa, Protein from Human)
- Splicing factor 3b subunit 1 (146 kDa, Protein from Human)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Rna-binding motif protein, x-linked 2 (37 kDa, Protein from Human)
- Splicing factor 3b subunit 3 (135 kDa, Protein from Human)
- U5 small nuclear ribonucleoprotein 40 kda protein (39 kDa, Protein from Human)
- U2 small nuclear ribonucleoprotein b'' (25 kDa, Protein from Human)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Human)
- U5 small nuclear ribonucleoprotein 200 kda helicase (244 kDa, Protein from Human)
- Human pre-bact-2 spliceosome (Complex from Homo sapiens)
- Crooked neck-like protein 1 (100 kDa, Protein from Human)
- Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Human)
- Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from Human)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Human)
- Magnesium ion (24 Da, Ligand)
- Splicing factor 3b subunit 4 (44 kDa, Protein from Human)
- U6 snrna (34 kDa, RNA from Human)
- Bud13 homolog (70 kDa, Protein from Human)
- Phd finger-like domain-containing protein 5a (12 kDa, Protein from Human)
- U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Human)
- Ubiquitin-like protein 5 (8 kDa, Protein from Human)
- Protein bud31 homolog (17 kDa, Protein from Human)
Human C Complex Spliceosome - High-resolution CORE
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6zym
Q-score: 0.498
Bertram K, El Ayoubi L, Dybkov O, Agafonov DE, Will CL, Hartmuth K, Urlaub H, Kastner B, Stark H, Luhrmann R
Mol Cell (2020) 80 pp. 127-139.e6 [ DOI: doi:10.1016/j.molcel.2020.09.012 Pubmed: 33007253 ]
- 116 kda u5 small nuclear ribonucleoprotein component (107 kDa, Protein from Human)
- Inositol hexakisphosphate (660 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Pre-mrna-splicing factor rbm22 (25 kDa, Protein from Human)
- Pre-mrna-splicing factor cwc25 homolog (49 kDa, Protein from Human)
- U6 snrna (25 kDa, RNA from Human)
- Wd repeat-containing protein 70 (73 kDa, Protein from Human)
- Peptidyl-prolyl cis-trans isomerase-like 1 (18 kDa, Protein from Human)
- Pre-mrna-splicing factor atp-dependent rna helicase prp16 (140 kDa, Protein from Human)
- Snw domain-containing protein 1 (61 kDa, Protein from Human)
- Pre-mrna-processing factor 17 (65 kDa, Protein from Human)
- Pre-mrna (103 kDa, RNA from Human)
- Protein frg1 (29 kDa, Protein from Human)
- Splicing factor yju2 (21 kDa, Protein from Human)
- Corepressor interacting with rbpj 1 (52 kDa, Protein from Human)
- U2 snrna (60 kDa, RNA from Human)
- Pre-mrna-processing-splicing factor 8 (207 kDa, Protein from Human)
- Pleiotropic regulator 1 (57 kDa, Protein from Human)
- Serine/arginine repetitive matrix protein 2 (300 kDa, Protein from Human)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- U5 snrna (36 kDa, RNA from Human)
- U5 small nuclear ribonucleoprotein 40 kda protein (39 kDa, Protein from Human)
- Crooked neck-like protein 1 (100 kDa, Protein from Human)
- Pre-mrna-splicing factor cwc22 homolog (105 kDa, Protein from Human)
- Magnesium ion (24 Da, Ligand)
- Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from Human)
- Pre-mrna-splicing factor isy1 homolog (33 kDa, Protein from Human)
- Human c complex spliceosome - high resolution core (Complex from Homo sapiens)
- Cell division cycle 5-like protein (92 kDa, Protein from Human)
- Protein bud31 homolog (17 kDa, Protein from Human)
human Bact spliceosome core structure
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6ff4
Q-score: 0.443
Haselbach D, Komarov I, Agafonov DE, Hartmuth K, Graf B, Dybkov O, Urlaub H, Kastner B, Luhrmann R, Stark H
Cell (2018) 172 pp. 454-464.e11 [ Pubmed: 29361316 DOI: doi:10.1016/j.cell.2018.01.010 ]
- Cell division cycle 5-like protein (92 kDa, Protein from Homo sapiens)
- Pre mrna (153 kDa, RNA from Homo sapiens)
- Pre-mrna-splicing factor rbm22 (46 kDa, Protein from Homo sapiens)
- Splicing factor 3b subunit 1 (146 kDa, Protein from Homo sapiens)
- Bud13 homolog (70 kDa, Protein from Homo sapiens)
- Human bact spliceosome state 1 unmasked (4 MDa, Complex from Homo sapiens)
- Splicing factor 3a subunit 2 (49 kDa, Protein from Homo sapiens)
- Snw domain-containing protein 1 (61 kDa, Protein from Homo sapiens)
- Splicing factor 3b subunit 6 (14 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Protein bud31 homolog (17 kDa, Protein from Homo sapiens)
- U6 snrna (34 kDa, RNA from Homo sapiens)
- Rna-binding motif protein, x-linked 2 (37 kDa, Protein from Homo sapiens)
- U2 snrna (60 kDa, RNA from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from Homo sapiens)
- Phd finger-like domain-containing protein 5a (12 kDa, Protein from Homo sapiens)
- Serine/arginine repetitive matrix protein 1 (102 kDa, Protein from Homo sapiens)
- Ring finger protein 113a (38 kDa, Protein from Homo sapiens)
- Pre-mrna-processing factor 17 (65 kDa, Protein from Homo sapiens)
- U5 snrna (36 kDa, RNA from Homo sapiens)
- Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from Homo sapiens)
- Splicing factor 3b subunit 3 (135 kDa, Protein from Homo sapiens)
- Inositol hexakisphosphate (660 Da, Ligand)
- Pleiotropic regulator 1 (57 kDa, Protein from Homo sapiens)
- Splicing factor 3b subunit 5 (10 kDa, Protein from Homo sapiens)
- Peptidyl-prolyl cis-trans isomerase-like 1 (18 kDa, Protein from Homo sapiens)
- 116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Splicing factor 3b subunit 2 (100 kDa, Protein from Homo sapiens)
- Serine/arginine repetitive matrix protein 2 (300 kDa, Protein from Homo sapiens)
- Crooked neck-like protein 1 (100 kDa, Protein from Homo sapiens)
- Peptidyl-prolyl cis-trans isomerase cwc27 homolog (53 kDa, Protein from Homo sapiens)
Cryo-EM structure of a human spliceosome activated for step 2 of splicing (C* complex)
Resolution: 5.9 Å
EM Method: Single-particle
Fitted PDBs: 5mqf
Q-score: 0.202
Bertram K, Agafonov DE, Liu WT, Dybkov O, Will CL, Hartmuth K, Urlaub H, Kastner B, Stark H, Lu Hrmann R
Nature (2017) 542 pp. 318-323 [ Pubmed: 28076346 DOI: doi:10.1038/nature21079 ]
- Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from Human)
- Human c* spliceosome, masked refinement (Complex from Homo sapiens)
- Peptidyl-prolyl cis-trans isomerase e (33 kDa, Protein from Human)
- U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Human)
- Minx pre-mrna (intron) (104 kDa, RNA from Human)
- Pre-mrna-splicing factor spf27 (26 kDa, Protein from Human)
- Homo sapiens rna, u6 small nuclear 1 (rnu6-1), small nuclear rna (34 kDa, RNA from Human)
- Human gene for small nuclear rna u2 (snrna u2) (60 kDa, RNA from Human)
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Human)
- Peptidyl-prolyl cis-trans isomerase-like 1 (18 kDa, Protein from Human)
- Pleiotropic regulator 1 (57 kDa, Protein from Human)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Human)
- 116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from Human)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Human)
- Snw domain-containing protein 1 (61 kDa, Protein from Human)
- Pre-mrna-processing factor 17 (65 kDa, Protein from Human)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Human)
- Atp-dependent rna helicase dhx8 (139 kDa, Protein from Human)
- Pre-mrna-splicing factor rbm22 (46 kDa, Protein from Human)
- Serine/arginine repetitive matrix protein 2 (300 kDa, Protein from Human)
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from Human)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Human)
- U5 small nuclear ribonucleoprotein 40 kda protein (39 kDa, Protein from Human)
- U2 small nuclear ribonucleoprotein b'' (25 kDa, Protein from Human)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Human)
- Crooked neck-like protein 1 (100 kDa, Protein from Human)
- Pre-mrna-splicing factor cwc22 homolog (105 kDa, Protein from Human)
- Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Human)
- Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from Human)
- Eukaryotic initiation factor 4a-iii (46 kDa, Protein from Human)
- Intron-binding protein aquarius (173 kDa, Protein from Human)
- Pre-mrna-splicing factor syf2 (28 kDa, Protein from Human)
- Homo sapiens u5 a small nuclear rna (36 kDa, RNA from Human)
- Pre-mrna-processing factor 19 (55 kDa, Protein from Human)
- Cell division cycle 5-like protein (92 kDa, Protein from Human)
- Protein bud31 homolog (17 kDa, Protein from Human)