E. coli 70S ribosome with an improved MS2 Tag inserted in H98 (Composite Map)
Resolution: 1.85 Å
EM Method: Single-particle
Fitted PDBs: 8fto
Q-score: 0.722
Nissley AJ, Kamal TS, Cate JHD
RNA (2023) 29 pp. 1500-1508 [ DOI: doi:10.1261/rna.079690.123 Pubmed: 37419664 ]
- P-site trna-fmet (24 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- 30s subunit (Complex from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
- 23s rrna (952 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- N-formylmethionine (177 Da, Ligand)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- Mrna (8 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- Mrna (Complex from Escherichia coli)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
- Trna (Complex from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 50s subunit (Complex from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- Ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
- E. coli 70s ribosome (Complex)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 16s rrna (499 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
E. coli C-P lyase bound to a PhnK/PhnL dual ABC dimer and ADP + Pi
Resolution: 1.93 Å
EM Method: Single-particle
Fitted PDBs: 7z15
Q-score: 0.688
Amstrup SK, Ong SC, Sofos N, Karlsen JL, Skjerning RB, Boesen T, Enghild JJ, Hove-Jensen B, Brodersen DE
Nat Commun (2023) 14 pp. 1001-1001 [ Pubmed: 36813778 DOI: doi:10.1038/s41467-023-36604-y ]
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Putative phosphonates utilization atp-binding protein phnk (31 kDa, Protein from Escherichia coli)
- Alpha-d-ribose 1-methylphosphonate 5-triphosphate synthase subunit phni (38 kDa, Protein from Escherichia coli)
- Alpha-d-ribose-1,2-cyclic-phosphate-5-phosphate (292 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Alpha-d-ribose 1-methylphosphonate 5-triphosphate synthase subunit phng (16 kDa, Protein from Escherichia coli)
- Alpha-d-ribose 1-methylphosphonate 5-triphosphate synthase subunit phnl (24 kDa, Protein from Escherichia coli)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Water (18 Da, Ligand)
- Alpha-d-ribose 1-methylphosphonate 5-phosphate c-p lyase (31 kDa, Protein from Escherichia coli)
- Phosphate ion (94 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Alpha-d-ribose 1-methylphosphonate 5-triphosphate synthase subunit phnh (21 kDa, Protein from Escherichia coli)
- E. coli c-p lyase bound to a phnk/phnl dual abc dimer and adp + pi (327 kDa, Complex from Escherichia coli)
E. coli C-P lyase bound to a PhnK ABC dimer and ATP
Resolution: 1.98 Å
EM Method: Single-particle
Fitted PDBs: 7z18
Q-score: 0.666
Amstrup SK, Ong SC, Sofos N, Karlsen JL, Skjerning RB, Boesen T, Enghild JJ, Hove-Jensen B, Brodersen DE
Nat Commun (2023) 14 pp. 1001-1001 [ Pubmed: 36813778 DOI: doi:10.1038/s41467-023-36604-y ]
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Putative phosphonates utilization atp-binding protein phnk (31 kDa, Protein from Escherichia coli)
- Alpha-d-ribose 1-methylphosphonate 5-triphosphate synthase subunit phni (38 kDa, Protein from Escherichia coli)
- Alpha-d-ribose-1,2-cyclic-phosphate-5-phosphate (292 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Alpha-d-ribose 1-methylphosphonate 5-triphosphate synthase subunit phng (16 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- Alpha-d-ribose 1-methylphosphonate 5-phosphate c-p lyase (31 kDa, Protein from Escherichia coli)
- E. coli c-p lyase bound to a phnk abc dimer and atp (277 kDa, Complex from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Alpha-d-ribose 1-methylphosphonate 5-triphosphate synthase subunit phnh (21 kDa, Protein from Escherichia coli)