Cryo-EM structure of the apo TPP riboswitch embedded in an RNA scaffold
Cryo-EM Structure of a group IIC intron embedded in an RNP scaffold
Cryo-EM structure of the Rail RNA motif
Haack DB, Rudolfs B, Jin S, Weeks KM, Toor N
bioRxiv (2024) [ Pubmed: 38915706 DOI: doi:10.1101/2024.06.10.598011 ]
- Rna (200-mer) (192 kDa, RNA from Clostridium acetobutylicum)
- Bacterial raia rna motif (Cellular component from Clostridium acetobutylicum)
- Magnesium ion (24 Da, Ligand)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9jm0
Q-score: 0.492
Wang Y, Wang C, Guan Z, Cao J, Xu J, Wang S, Cui Y, Wang Q, Chen Y, Yin Y, Zhang D, Liu H, Sun M, Jin S, Tao P, Zou T
Cell Rep (2024) 43 pp. 114857-114857 [ DOI: doi:10.1016/j.celrep.2024.114857 Pubmed: 39395169 ]
- Retron ec86-effector fiber (Complex from Escherichia coli)
- [(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2r,3s,4r,5s)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate (559 Da, Ligand)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Rna (82-mer) (26 kDa, RNA from Escherichia coli)
- Retron ec86 putative ribosyltransferase/dna-binding protein (35 kDa, Protein from Escherichia coli)
- Retron ec86 reverse transcriptase (37 kDa, Protein from Escherichia coli)
- Nicotinamide (122 Da, Ligand)
- Rna (5'-r(p*cp*gp*up*ap*ap*gp*gp*gp*up*gp*cp*gp*cp*a)-3') (4 kDa, RNA from Escherichia coli)
Cryo-EM structure of a group IIC intron RNA
Resolution: 2.56 Å
EM Method: Single-particle
Fitted PDBs: 9c6i
Q-score: 0.557
Haack DB, Rudolfs B, Jin S, Khitun A, Weeks KM, Toor N
Nat Commun (2025) 16 pp. 880-880 [ DOI: doi:10.1038/s41467-024-55699-5 Pubmed: 39837824 ]
- Group iic intron (135 kDa, RNA from Oceanobacillus iheyensis)
- Magnesium ion (24 Da, Ligand)
- Group iic intron (135 kDa, Complex from Oceanobacillus iheyensis)
Group IIC intron embedded with the TPP riboswitch
Resolution: 2.41 Å
EM Method: Single-particle
Fitted PDBs: 9c6j
Q-score: 0.581
Haack DB, Rudolfs B, Jin S, Khitun A, Weeks KM, Toor N
Nat Commun (2025) 16 pp. 880-880 [ DOI: doi:10.1038/s41467-024-55699-5 Pubmed: 39837824 ]
- Group iic intron embedded with the tpp riboswitch (160 kDa, RNA from Oceanobacillus iheyensis)
- Group iic intron embedded with the tpp riboswitch (160 kDa, Complex from Oceanobacillus iheyensis)
- Magnesium ion (24 Da, Ligand)
Cryo-EM structure of the TPP riboswitch embedded in an RNA scaffold bound to thiamine pyrophosphate
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 9c6k
Q-score: 0.453
Haack DB, Rudolfs B, Jin S, Khitun A, Weeks KM, Toor N
Nat Commun (2025) 16 pp. 880-880 [ DOI: doi:10.1038/s41467-024-55699-5 Pubmed: 39837824 ]
- Sodium ion (22 Da, Ligand)
- Tpp riboswitch embedded in an rna scaffold bound to thiamine pyrophosphate (161 kDa, RNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Tpp riboswitch embedded in an rna scaffold bound with thiamine pyrophosphate (27 kDa, Complex from Escherichia coli)
- Thiamine diphosphate (425 Da, Ligand)
Human URAT1 bound with Uric acid
Resolution: 3.32 Å
EM Method: Single-particle
Fitted PDBs: 9jdv
Q-score: 0.344
Wu C, Zhang C, Jin S, Wang JJ, Dai A, Xu J, Zhang H, Yang X, He X, Yuan Q, Hu W, Xu Y, Wang M, Jiang Y, Yang D, Xu HE
bioRxiv (2024) [ DOI: doi:10.1101/2024.09.11.612394 ]
- Water (18 Da, Ligand)
- Solute carrier family 22 member 12 (59 kDa, Protein from Homo sapiens)
- Uric acid (168 Da, Ligand)
- Human uric acid transporter 1 with uric acid (Complex from Homo sapiens)
Human URAT1 bound with verinurad
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 9jdy
Q-score: 0.386
Wu C, Zhang C, Jin S, Wang JJ, Dai A, Xu J, Zhang H, Yang X, He X, Yuan Q, Hu W, Xu Y, Wang M, Jiang Y, Yang D, Xu HE
bioRxiv (2024) [ DOI: doi:10.1101/2024.09.11.612394 ]
- Verinurad (348 Da, Ligand)
- Human uric acid transportor 1 with verinurad (Complex from Homo sapiens)
- Solute carrier family 22 member 12 (59 kDa, Protein from Homo sapiens)