Structural organization of a late activated human spliceosome (Baqr, core region)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7qtt
Q-score: 0.384
Schmitzova J, Cretu C, Dienemann C, Urlaub H, Pena V
Nature (2023) 617 pp. 842-850 [ DOI: doi:10.1038/s41586-023-06049-w Pubmed: 37165190 ]
- Putative pre-mrna-splicing factor atp-dependent rna helicase dhx16 (119 kDa, Protein from human)
- Pre-mrna-splicing factor cwc22 homolog (105 kDa, Protein from human)
- U2snrna (60 kDa, RNA from human)
- Crooked neck-like protein 1 (100 kDa, Protein from human)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from human)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from human)
- Phd finger-like domain-containing protein 5a (12 kDa, Protein from human)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Inositol hexakisphosphate (660 Da, Ligand)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from human)
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from human)
- Pleiotropic regulator 1 (57 kDa, Protein from human)
- Snw domain-containing protein 1 (61 kDa, Protein from human)
- Peptidyl-prolyl cis-trans isomerase-like 1 (18 kDa, Protein from human)
- Late human activated spliceosome arrested with a dominant-negative mutant of the splicing helicase aquarius (aquarius k829a) (Complex from Homo sapiens)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from human)
- Splicing factor 3a subunit 2 (49 kDa, Protein from human)
- Splicing factor 3b subunit 1 (146 kDa, Protein from human)
- Bud13 homolog (70 kDa, Protein from human)
- Zinc ion (65 Da, Ligand)
- Ring-type e3 ubiquitin-protein ligase ppil2 (58 kDa, Protein from human)
- G-patch domain and kow motifs-containing protein (52 kDa, Protein from human)
- Peptidyl-prolyl cis-trans isomerase-like 4 (57 kDa, Protein from human)
- Cell division cycle 5-like protein (92 kDa, Protein from human)
- Splicing factor 3b subunit 2 (100 kDa, Protein from human)
- Minx (102 kDa, RNA from unidentified adenovirus)
- Splicing factor 3b subunit 3 (135 kDa, Protein from human)
- U6snrna (34 kDa, RNA from Homo sapiens)
- Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from human)
- Pre-mrna-splicing factor rbm22 (46 kDa, Protein from human)
- Magnesium ion (24 Da, Ligand)
- Splicing factor 3b subunit 4 (44 kDa, Protein from human)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from human)
- 116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from human)
- Protein bud31 homolog (17 kDa, Protein from human)
- Ring finger protein 113a (38 kDa, Protein from human)
- Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from human)
- Splicing factor 3b subunit 5 (10 kDa, Protein from human)
- Splicing factor 3a subunit 3 (58 kDa, Protein from human)
- Serine/arginine repetitive matrix protein 2 (300 kDa, Protein from human)
- Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from human)
- U5 snrna (37 kDa, RNA from human)
Resolution: 5.9 Å
EM Method: Single-particle
Fitted PDBs: 8ch6
Q-score: 0.154
Schmitzova J, Cretu C, Dienemann C, Urlaub H, Pena V
Nature (2023) 617 pp. 842-850 [ DOI: doi:10.1038/s41586-023-06049-w Pubmed: 37165190 ]
- U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from human)
- Rnu5a-1 (37 kDa, RNA from human)
- Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from human)
- Ring finger protein 113a (38 kDa, Protein from human)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from human)
- Pre-mrna-processing factor 17 (65 kDa, Protein from human)
- Snw domain-containing protein 1 (61 kDa, Protein from human)
- Splicing factor 3b subunit 5 (10 kDa, Protein from human)
- Cell division cycle 5-like protein (92 kDa, Protein from human)
- U5 small nuclear ribonucleoprotein 200 kda helicase (244 kDa, Protein from human)
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from human)
- Pre-mrna-splicing factor cwc22 homolog (105 kDa, Protein from human)
- Rnu2-1 (60 kDa, RNA from human)
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from human)
- Pre-mrna-splicing factor spf27 (26 kDa, Protein from human)
- Peptidyl-prolyl cis-trans isomerase e (33 kDa, Protein from human)
- Inositol hexakisphosphate (660 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Pre-mrna-splicing factor rbm22 (46 kDa, Protein from human)
- Peptidyl-prolyl cis-trans isomerase-like 4 (57 kDa, Protein from human)
- Splicing factor 3b subunit 4 (44 kDa, Protein from human)
- Magnesium ion (24 Da, Ligand)
- Splicing factor 3b subunit 1 (146 kDa, Protein from human)
- Crooked neck-like protein 1 (100 kDa, Protein from human)
- Late human activated spliceosome arrested with a dominant-negative mutant of the splicing helicase aquarius (aquarius k829a) (Complex from Homo sapiens)
- Intron-binding protein aquarius (171 kDa, Protein from human)
- G-patch domain and kow motifs-containing protein (52 kDa, Protein from human)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from human)
- Splicing factor 3a subunit 3 (58 kDa, Protein from human)
- Rnu6-1 (34 kDa, RNA from Homo sapiens)
- Pre-mrna-splicing factor isy1 homolog (33 kDa, Protein from human)
- Phd finger-like domain-containing protein 5a (12 kDa, Protein from human)
- Splicing factor 3a subunit 1 (88 kDa, Protein from human)
- Pre-mrna-processing factor 19 (55 kDa, Protein from human)
- Minx-m3 (102 kDa, RNA from unidentified adenovirus)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from human)
- Peptidyl-prolyl cis-trans isomerase-like 1 (18 kDa, Protein from human)
- U5 small nuclear ribonucleoprotein 40 kda protein (39 kDa, Protein from human)
- Splicing factor 3b subunit 3 (135 kDa, Protein from human)
- Zinc ion (65 Da, Ligand)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from human)
- Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from human)
- Putative pre-mrna-splicing factor atp-dependent rna helicase dhx16 (119 kDa, Protein from human)
- Ring-type e3 ubiquitin-protein ligase ppil2 (58 kDa, Protein from human)
- Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from human)
- Pleiotropic regulator 1 (57 kDa, Protein from human)
- Bud13 homolog (70 kDa, Protein from human)
- 116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from human)
- Protein bud31 homolog (17 kDa, Protein from human)
- Serine/arginine repetitive matrix protein 2 (300 kDa, Protein from human)
- Splicing factor 3b subunit 2 (100 kDa, Protein from human)
- U2 small nuclear ribonucleoprotein b'' (25 kDa, Protein from human)
- Splicing factor 3a subunit 2 (49 kDa, Protein from human)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from human)
Dimeric form of SARS-CoV-2 RNA-dependent RNA polymerase
Resolution: 5.5 Å
EM Method: Single-particle
Fitted PDBs: 7oyg
Q-score: 0.151
Jochheim FA, Tegunov D, Hillen HS, Schmitzova J, Kokic G, Dienemann C, Cramer P
Communications Biology (2021) 4 pp. 999- [ DOI: doi:10.1038/s42003-021-02529-9 ]
- Dimeric form of sars-cov-2 rna-dependent rna polymerase complex (nsp12, nsp7, nsp8) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(p*up*gp*cp*ap*cp*up*gp*cp*gp*up*ap*g)-3') (18 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase (nsp12) (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Rna (5'-r(p*cp*up*ap*cp*gp*cp*ap*gp*up*g)-3') (4 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 RdRp with Molnupiravir/ NHC in the template strand base-paired with A
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7ozu
Q-score: 0.522
Kabinger F, Stiller C, Schmitzova J, Dienemann C, Kokic G, Hillen HS, Hobartner C, Cramer P
Nat Struct Mol Biol (2021) 28 pp. 740-746 [ DOI: doi:10.1038/s41594-021-00651-0 Pubmed: 34381216 ]
- Non-structural protein 8 (24 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Product rna (10 kDa, RNA from synthetic construct)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rdrp (183 MDa, Complex)
- Replicase polyprotein 1ab (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Template rna (10 kDa, RNA from synthetic construct)
SARS-CoV-2 RdRp with Molnupiravir/ NHC in the template strand base-paired with G
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7ozv
Q-score: 0.525
Kabinger F, Stiller C, Schmitzova J, Dienemann C, Kokic G, Hillen HS, Hobartner C, Cramer P
Nat Struct Mol Biol (2021) 28 pp. 740-746 [ DOI: doi:10.1038/s41594-021-00651-0 Pubmed: 34381216 ]
- Non-structural protein 8 (24 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rdrp (183 MDa, Complex)
- Product rna (10 kDa, RNA from synthetic construct)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template rna (10 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Replicase polyprotein 1ab (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7b3b
Q-score: 0.501
Kokic G, Hillen HS, Tegunov D, Dienemann C, Seitz F, Schmitzova J, Farnung L, Siewert A, Hobartner C, Cramer P
Nat Commun (2021) 12 pp. 279-279 [ DOI: doi:10.1038/s41467-020-20542-0 Pubmed: 33436624 ]
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase nsp12 (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp7 and nsp8 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase (nsp12) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Rna (5'-r(p*up*gp*cp*ap*up*cp*gp*cp*gp*up*ap*g)-3') (18 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Dna and rna (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase complex (nsp12, nsp7, nsp8) with elongation scaffold containing remdesivir at position -3. (Complex)
- Dna/rna (5'-r(p*cp*up*ap*cp*gp*cp*g)-d(p*(rmp))-r(p*up*g)-3') (4 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7b3c
Q-score: 0.455
Kokic G, Hillen HS, Tegunov D, Dienemann C, Seitz F, Schmitzova J, Farnung L, Siewert A, Hobartner C, Cramer P
Nat Commun (2021) 12 pp. 279-279 [ DOI: doi:10.1038/s41467-020-20542-0 Pubmed: 33436624 ]
- Dna/rna (5'-r(p*cp*up*ap*cp*gp*cp*a)-d(p*(rmp))-r(p*gp*up*g)-3') (4 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp7 and 8 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(p*up*cp*ap*cp*up*up*gp*cp*gp*up*ap*g)-3') (18 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Dna and rna (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase (nsp12) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase nsp12 (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase complex (nsp12, nsp7, nsp8) with elongation scaffold containing remdesivir at position -4. (Complex)
- Zinc ion (65 Da, Ligand)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7b3d
Q-score: 0.558
Kokic G, Hillen HS, Tegunov D, Dienemann C, Seitz F, Schmitzova J, Farnung L, Siewert A, Hobartner C, Cramer P
Nat Commun (2021) 12 pp. 279-279 [ DOI: doi:10.1038/s41467-020-20542-0 Pubmed: 33436624 ]
- Sars-cov-2 rna-dependent rna polymerase nsp12 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase nsp12 (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase complex (nsp12, nsp7, nsp8) with elongation scaffold containing amp at position -4. (Complex)
- Sars-cov-2 nsp7 and 8 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(p*up*gp*cp*ap*cp*up*gp*cp*gp*up*ap*g)-3') (18 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Dna and rna (Complex from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Rna (5'-r(p*cp*up*ap*cp*gp*cp*ap*gp*up*g)-3') (4 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)