Cryo-EM structure of Tetrahymena ribozyme conformation 4 undergoing the second-step self-splicing
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 7ygc
Q-score: 0.454
Li S, Palo MZ, Zhang X, Pintilie G, Zhang K
Nat Commun (2023) 14 pp. 1294-1294 [ DOI: doi:10.1038/s41467-023-36724-5 Pubmed: 36928031 ]
- Rna (5'-r(*up*cp*g)-3') (911 Da, RNA from Tetrahymena thermophila)
- Magnesium ion (24 Da, Ligand)
- Rna (393-mer) (127 kDa, RNA from Tetrahymena thermophila)
- Rna (5'-r(*cp*cp*cp*up*cp*up*up*ap*ap*cp*c)-3') (3 kDa, RNA from Tetrahymena thermophila)
- Cryo-em structure of tetrahymena ribozyme conformation 4 undergoing the second-step self-splicing (130 kDa, Complex from Tetrahymena)
Misfolded Tetrahymena ribozyme conformation 1
Resolution: 3.53 Å
EM Method: Single-particle
Fitted PDBs: 7xsk
Q-score: 0.302
Li S, Palo MZ, Pintilie G, Zhang X, Su Z, Kappel K, Chiu W, Zhang K, Das R
PNAS (2022) 119 pp. e2209146119-e2209146119 [ DOI: doi:10.1073/pnas.2209146119 Pubmed: 36067294 ]
- Rna (388-mer) (125 kDa, RNA from Tetrahymena thermophila)
- Misfolded tetrahymena ribozyme conformation 1 (120 kDa, Complex from Tetrahymena thermophila)
Misfolded Tetrahymena ribozyme conformation 2
Resolution: 3.84 Å
EM Method: Single-particle
Fitted PDBs: 7xsl
Q-score: 0.279
Li S, Palo MZ, Pintilie G, Zhang X, Su Z, Kappel K, Chiu W, Zhang K, Das R
PNAS (2022) 119 pp. e2209146119-e2209146119 [ Pubmed: 36067294 DOI: doi:10.1073/pnas.2209146119 ]
- Rna (388-mer) (125 kDa, RNA from Tetrahymena thermophila)
- Misfolded tetrahymena ribozyme conformation 2 (120 kDa, Complex from Tetrahymena thermophila)
Misfolded Tetrahymena ribozyme conformation 3
Resolution: 4.01 Å
EM Method: Single-particle
Fitted PDBs: 7xsm
Q-score: 0.261
Li S, Palo MZ, Pintilie G, Zhang X, Su Z, Kappel K, Chiu W, Zhang K, Das R
PNAS (2022) 119 pp. e2209146119-e2209146119 [ DOI: doi:10.1073/pnas.2209146119 Pubmed: 36067294 ]
- Rna (388-mer) (125 kDa, RNA from Tetrahymena thermophila)
- Misfolded tetrahymena ribozyme conformation 3 (120 kDa, Complex from Tetrahymena thermophila)
Native Tetrahymena ribozyme conformation
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 7xsn
Q-score: 0.416
Li S, Palo MZ, Pintilie G, Zhang X, Su Z, Kappel K, Chiu W, Zhang K, Das R
PNAS (2022) 119 pp. e2209146119-e2209146119 [ DOI: doi:10.1073/pnas.2209146119 Pubmed: 36067294 ]
- Rna (387-mer) (125 kDa, RNA from Tetrahymena thermophila)
- Native tetrahymena ribozyme conformation (120 kDa, Complex from Tetrahymena thermophila)
Structure of outer-arm dyneins bound to microtubule with microtubule binding state 1(MTBS-1)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7k58
Q-score: 0.357
Rao Q, Han L, Wang Y, Chai P, Kuo YW, Yang R, Hu F, Yang Y, Howard J, Zhang K
Nat Struct Mol Biol (2021) 28 pp. 799-810 [ DOI: doi:10.1038/s41594-021-00656-9 Pubmed: 34556869 ]
- Thioredoxin (12 kDa, Protein from Tetrahymena thermophila)
- Dynein intermediate chain 2 (69 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain (11 kDa, Protein from Tetrahymena thermophila)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila)
- Flagellar outer dynein arm intermediate protein, putative (63 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain 2a (14 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain tctex-type 1 protein (12 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain (11 kDa, Protein from Tetrahymena thermophila)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Outer arm dynein beta heavy chain (529 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain roadblock-type 2 protein (12 kDa, Protein from Tetrahymena thermophila)
- Magnesium ion (24 Da, Ligand)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila)
- Outer-arm dynein (2 MDa, Complex from Tetrahymena thermophila)
- Dynein light chain roadblock (10 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain (11 kDa, Protein from Tetrahymena thermophila)
- Dynein heavy chain, outer arm protein (533 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain 1 (21 kDa, Protein from Tetrahymena thermophila)
- Gamma heavy chain (450 kDa, Protein from Tetrahymena thermophila)
Structure of outer-arm dynein bound to microtubule doublet in microtubule binding state 2 (MTBS-2)
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7k5b
Q-score: 0.264
Rao Q, Han L, Wang Y, Chai P, Kuo YW, Yang R, Hu F, Yang Y, Howard J, Zhang K
Nat Struct Mol Biol (2021) 28 pp. 799-810 [ DOI: doi:10.1038/s41594-021-00656-9 Pubmed: 34556869 ]
- Dynein heavy chain, outer arm protein (533 kDa, Protein from Tetrahymena thermophila)
- Thioredoxin (12 kDa, Protein from Tetrahymena thermophila)
- Dynein intermediate chain 2 (69 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain (11 kDa, Protein from Tetrahymena thermophila)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Outer-arm dynein bound to microtubule doublet in microtubule binding state 2 (mtbs-2) (Complex from Tetrahymena thermophila)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila)
- Flagellar outer dynein arm intermediate protein, putative (63 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain 2a (14 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain roadblock-type 2 protein (14 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain (12 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain (11 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila)
- Outer arm dynein beta heavy chain (529 kDa, Protein from Tetrahymena thermophila)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dynein light chain roadblock-type 2 protein (17 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain 1 (21 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain 4a (16 kDa, Protein from Tetrahymena thermophila)
- Magnesium ion (24 Da, Ligand)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila)
- Gamma heavy chain (450 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain tctex-type 1 protein (12 kDa, Protein from Tetrahymena thermophila)
Structure of the free outer-arm dynein in pre-parallel state
Resolution: 8.0 Å
EM Method: Single-particle
Fitted PDBs: 7kek
Q-score: 0.082
Rao Q, Han L, Wang Y, Chai P, Kuo YW, Yang R, Hu F, Yang Y, Howard J, Zhang K
Nat Struct Mol Biol (2021) 28 pp. 799-810 [ DOI: doi:10.1038/s41594-021-00656-9 Pubmed: 34556869 ]
- Dynein light chain roadblock lc7b (18 kDa, Protein from Tetrahymena thermophila)
- Dynein gamma heavy chain (475 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain lc8_1b (dlc82) (10 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain lc8_1a (lc10) (12 kDa, Protein from Tetrahymena thermophila)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dynein intermediate chain dic2 (77 kDa, Protein from Tetrahymena thermophila)
- Dynein intermediate chain dic3 (77 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain lc8_3b (12 kDa, Protein from Tetrahymena thermophila)
- Dynein beta heavy chain (530 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain lc8_3a (10 kDa, Protein from Tetrahymena thermophila)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dynein light chain tctex_b (13 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain tctex_a (lc2a) (15 kDa, Protein from Tetrahymena thermophila)
- Thioredoxin lc3bl (14 kDa, Protein from Tetrahymena thermophila)
- Dynein alpha heavy chain (534 kDa, Protein from Tetrahymena thermophila)
- Free outer-arm dynein (Complex from Tetrahymena thermophila)
- Dynein light chain lc8_2b (13 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain lc8_2a (lc8e) (10 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain 1 (22 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain roadblock lc7a (14 kDa, Protein from Tetrahymena thermophila)
16-nm repeat microtubule doublet
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7mwg
Q-score: 0.438
Rao Q, Han L, Wang Y, Chai P, Kuo YW, Yang R, Hu F, Yang Y, Howard J, Zhang K
Nat Struct Mol Biol (2021) 28 pp. 799-810 [ DOI: doi:10.1038/s41594-021-00656-9 Pubmed: 34556869 ]
- Tubulin alpha chain (49 kDa, Protein from Tetrahymena thermophila)
- Water (18 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Tubulin beta chain (49 kDa, Protein from Tetrahymena thermophila)
- Magnesium ion (24 Da, Ligand)
- 16-nm repeat microtubule doublet (Complex from Tetrahymena thermophila)
Apo L-21 ScaI Tetrahymena ribozyme
Resolution: 3.14 Å
EM Method: Single-particle
Fitted PDBs: 7ez0
Q-score: 0.425