Tetrahymena ribozyme with water and magnesium ions
Resolution: 2.31 Å
EM Method: Single-particle
Fitted PDBs: 9cbw, 9cby
Q-score: 0.5455
Kretsch RC, Li S, Pintilie G, Palo MZ, Case DA, Das R, Chiu W
To Be Published
- Rna (387-mer) (125 kDa, RNA from Tetrahymena thermophila)
- Water (18 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Apo l-21 scai tetrahymena ribozyme with water and metal ions. (125 kDa, Complex from Tetrahymena thermophila)
Tetrahymena ribozyme with water and magnesium ions
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 9cbu, 9cbx
Q-score: 0.5565
Kretsch RC, Li S, Pintilie G, Palo MZ, Case DA, Das R, Chiu W
To Be Published
- Rna (387-mer) (125 kDa, RNA from Tetrahymena thermophila)
- Water (18 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Apo l-21 scai tetrahymena ribozyme with water and metal ions. (125 kDa, Complex from Tetrahymena thermophila)
48S late-stage initiation complex with m6A mRNA
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 8p03
Q-score: 0.509
Guca E, Alarcon R, Palo MZ, Santos L, Alonso-Gil S, Davyt M, de Lima LHF, Boissier F, Das S, Zagrovic B, Puglisi JD, Hashem Y, Ignatova Z
Mol Cell (2024) 84 pp. 584-595.e6 [ DOI: doi:10.1016/j.molcel.2023.12.028 Pubmed: 38244546 ]
- 40s ribosomal protein s29 (6 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l41 (3 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s4 (29 kDa, Protein from Oryctolagus cuniculus)
- Initiator methionylated trna (24 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein s6 (27 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein us15 (17 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein sa (23 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s9 (22 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s11 (18 kDa, Protein from Oryctolagus cuniculus)
- Eukaryotic translation initiation factor 4c (12 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s23 (15 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us13 (17 kDa, Protein from Oryctolagus cuniculus)
- M6a-methylated mrna (2 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein s21 (9 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s2 (29 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us10 (13 kDa, Protein from Oryctolagus cuniculus)
- 48s late-stage initiation complex with m6a-modified mrna (Complex from Oryctolagus cuniculus)
- 40s ribosomal protein es10 (11 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s25 (13 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s30 (14 kDa, Protein from Oryctolagus cuniculus)
- Atp binding cassette subfamily e member 1 (66 kDa, Protein from Oryctolagus cuniculus)
- Eukaryotic translation initiation factor 2 subunit 1 (32 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s26 (12 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us11 (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein es31 (8 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s3 (25 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s27 (9 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein es1 (24 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s24 (15 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein es19 (15 kDa, Protein from Oryctolagus cuniculus)
- 18s ribosomal rna (601 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein us9 (15 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s5 (21 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s28 (7 kDa, Protein from Oryctolagus cuniculus)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein us19 (17 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s15a (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein es7 (21 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s12 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein rack1 (34 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s8 (23 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein es17 (15 kDa, Protein from Oryctolagus cuniculus)
48S late-stage initiation complex with non methylated mRNA
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8p09
Q-score: 0.494
Guca E, Alarcon R, Palo MZ, Santos L, Alonso-Gil S, Davyt M, de Lima LHF, Boissier F, Das S, Zagrovic B, Puglisi JD, Hashem Y, Ignatova Z
Mol Cell (2024) 84 pp. 584-595.e6 [ DOI: doi:10.1016/j.molcel.2023.12.028 Pubmed: 38244546 ]
- 40s ribosomal protein s29 (6 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l41 (3 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s4 (29 kDa, Protein from Oryctolagus cuniculus)
- Initiator methionylated trna (24 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein s6 (27 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein us15 (17 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein sa (23 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s9 (22 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s11 (18 kDa, Protein from Oryctolagus cuniculus)
- Eukaryotic translation initiation factor 4c (12 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s23 (15 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us13 (17 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s21 (9 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s2 (29 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us10 (13 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein es10 (11 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s25 (13 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s30 (14 kDa, Protein from Oryctolagus cuniculus)
- Atp binding cassette subfamily e member 1 (66 kDa, Protein from Oryctolagus cuniculus)
- Eukaryotic translation initiation factor 2 subunit 1 (32 kDa, Protein from Oryctolagus cuniculus)
- 48s late-stage initiation complex with non methylated mrna (Complex from Oryctolagus cuniculus)
- 40s ribosomal protein s26 (12 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us11 (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein es31 (8 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s3 (25 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s27 (9 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein es1 (24 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s24 (15 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein es19 (15 kDa, Protein from Oryctolagus cuniculus)
- 18s ribosomal rna (601 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein us9 (15 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s5 (21 kDa, Protein from Oryctolagus cuniculus)
- Mrna (2 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein s28 (7 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us19 (17 kDa, Protein from Oryctolagus cuniculus)
- Magnesium ion (24 Da, Ligand)
- Ribosomal protein s15a (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein es7 (21 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s12 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein rack1 (34 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s8 (23 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein es17 (15 kDa, Protein from Oryctolagus cuniculus)
Cryo-EM structure of Tetrahymena ribozyme conformation 1 undergoing the first-step self-splicing
Resolution: 4.14 Å
EM Method: Single-particle
Fitted PDBs: 7yc8
Q-score: 0.261
Zhang X, Li S, Pintilie G, Palo MZ, Zhang K
Nucleic Acids Res (2023) 51 pp. 1317-1325 [ Pubmed: 36660826 DOI: doi:10.1093/nar/gkac1268 ]
- Rna (388-mer) (127 kDa, RNA from Tetrahymena)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Cryo-em structure of tetrahymena ribozyme conformation 1 undergoing the first-step self-splicing (130 kDa, Complex from Tetrahymena)
Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the first-step self-splicing
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 7ycg
Q-score: 0.359
Zhang X, Li S, Pintilie G, Palo MZ, Zhang K
Nucleic Acids Res (2023) 51 pp. 1317-1325 [ Pubmed: 36660826 DOI: doi:10.1093/nar/gkac1268 ]
- Rna (393-mer) (127 kDa, RNA from Tetrahymena)
- Magnesium ion (24 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Rna (5'-r(*cp*cp*cp*up*cp*up*ap*ap*ap*cp*c)-3') (3 kDa, RNA from Tetrahymena)
- Cryo-em structure of tetrahymena ribozyme conformation 2 undergoing the first-step self-splicing (130 kDa, Complex from Tetrahymena)
Cryo-EM structure of Tetrahymena ribozyme conformation 3 undergoing the first-step self-splicing
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7ych
Q-score: 0.373
Zhang X, Li S, Pintilie G, Palo MZ, Zhang K
Nucleic Acids Res (2023) 51 pp. 1317-1325 [ Pubmed: 36660826 DOI: doi:10.1093/nar/gkac1268 ]
- Rna (393-mer) (127 kDa, RNA from Tetrahymena)
- Cryo-em structure of tetrahymena ribozyme conformation 3 undergoing the first-step self-splicing (130 kDa, Complex from Tetrahymena)
- Magnesium ion (24 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Rna (5'-r(*cp*cp*cp*up*cp*up*ap*ap*ap*cp*c)-3') (3 kDa, RNA from Tetrahymena)
Cryo-EM structure of Tetrahymena ribozyme conformation 4 undergoing the first-step self-splicing
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 7yci
Q-score: 0.387
Zhang X, Li S, Pintilie G, Palo MZ, Zhang K
Nucleic Acids Res (2023) 51 pp. 1317-1325 [ Pubmed: 36660826 DOI: doi:10.1093/nar/gkac1268 ]
- Rna (389-mer) (127 kDa, RNA from Tetrahymena)
- Cryo-em structure of tetrahymena ribozyme conformation 4 undergoing the first-step self-splicing (130 kDa, Complex from Tetrahymena)
- Magnesium ion (24 Da, Ligand)
- Rna (5'-r(*cp*cp*cp*up*cp*u)-3') (1 kDa, RNA from Tetrahymena)
- Guanosine-5'-triphosphate (523 Da, Ligand)
Cryo-EM structure of Tetrahymena ribozyme conformation 5 undergoing the second-step self-splicing
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 7yg8
Q-score: 0.419
Li S, Palo MZ, Zhang X, Pintilie G, Zhang K
Nat Commun (2023) 14 pp. 1294-1294 [ Pubmed: 36928031 DOI: doi:10.1038/s41467-023-36724-5 ]
- Cryo-em structure of tetrahymena ribozyme conformation 5 undergoing the second-step self-splicing (130 kDa, Complex from Tetrahymena)
- Rna (5'-r(*up*cp*g)-3') (911 Da, RNA from Tetrahymena)
- Magnesium ion (24 Da, Ligand)
- Rna (387-mer) (127 kDa, RNA from Tetrahymena)
- Rna (5'-r(*cp*cp*cp*up*c)-3') (1 kDa, RNA from Tetrahymena)