Spraguea lophii ribosome in the closed conformation by cryo sub tomogram averaging
Resolution: 10.8 Å
EM Method: Subtomogram averaging
Fitted PDBs: 8p5d
Q-score: 0.088
McLaren M, Conners R, Isupov MN, Gil-Diez P, Gambelli L, Gold VAM, Walter A, Connell SR, Williams B, Daum B
Nat Microbiol (2023) 8 pp. 1834-1845 [ Pubmed: 37709902 DOI: doi:10.1038/s41564-023-01469-w ]
- 40s ribosomal protein s13 (16 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l6 (20 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s26 (11 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l31 (12 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s12 (14 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l3 (12 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s16 (16 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l23a (12 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s4 (31 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s11 (18 kDa, Protein from Spraguea lophii 42 110)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l44 (11 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l8 (27 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l7 (27 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l36 (11 kDa, Protein from Spraguea lophii 42 110)
- Rna 5s (38 kDa, RNA from Spraguea lophii 42 110)
- S60 ribosomal protein l10 (25 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l19 (19 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l11 (19 kDa, Protein from Spraguea lophii 42 110)
- Ribosomal protein l13a (22 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s8 (19 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s7 (19 kDa, Protein from Spraguea lophii 42 110)
- Ul15 (16 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l27 (18 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l26 (15 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s29 (7 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l39 (6 kDa, Protein from Spraguea lophii 42 110)
- Es27 (9 kDa, Protein from Spraguea lophii 42 110)
- Ubiquitin (14 kDa, Protein from Spraguea lophii 42 110)
- Ribosomal protein l34 (12 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l17 (19 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l20 (20 kDa, Protein from Spraguea lophii 42 110)
- Guanine nucleotide binding protein beta subunit (36 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s19 (16 kDa, Protein from Spraguea lophii 42 110)
- Es30 (6 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l3 (44 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s6 (26 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s5 (21 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s25 (14 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s10 (12 kDa, Protein from Spraguea lophii 42 110)
- Ribosomal protein s19 (18 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l32 (16 kDa, Protein from Spraguea lophii 42 110)
- Ribosomal protein s21e (7 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s3 (27 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l5 (33 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l4 (37 kDa, Protein from Spraguea lophii 42 110)
- Dnl-type domain-containing protein (17 kDa, Protein from Spraguea lophii 42 110)
- Es28 (7 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s9 (21 kDa, Protein from Spraguea lophii 42 110)
- Es1 (25 kDa, Protein from Spraguea lophii 42 110)
- Ribosomal protein l15 (24 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s2 (27 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l22 (12 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l21 (18 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s18 (18 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l8 (23 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s14 (14 kDa, Protein from Spraguea lophii 42 110)
- El37 (10 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s24 (17 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s0 (26 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l35a (12 kDa, Protein from Spraguea lophii 42 110)
- Ribosome (Complex from Spraguea lophii 42 110)
- 60s ribosomal protein l13 (19 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l18 (21 kDa, Protein from Spraguea lophii 42 110)
- Transposase (13 kDa, Protein from Spraguea lophii 42 110)
- Ubiquitin/40s ribosomal protein s27a fusion (16 kDa, Protein from Spraguea lophii 42 110)
- Ribosomal l29 protein (fragment),ribosomal l29 protein (fragment),ribosomal l29 protein (fragment),ribosomal l29 protein (14 kDa, Protein from Spraguea lophii 42 110)
- Us12 (15 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s15a (14 kDa, Protein from Spraguea lophii 42 110)
- Ribosomal protein l23 (15 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l9 (21 kDa, Protein from Spraguea lophii 42 110)
- Rna 28s (849 kDa, RNA from Spraguea lophii 42 110)
- Rna 16s (444 kDa, RNA from Spraguea lophii 42 110)
- Es17 (14 kDa, Protein from Spraguea lophii 42 110)
- 60s ribosomal protein l37a (10 kDa, Protein from Spraguea lophii 42 110)
- Ribosomal protein l24e (15 kDa, Protein from Spraguea lophii 42 110)
- 40s ribosomal protein s20 (13 kDa, Protein from Spraguea lophii 42 110)
Cryo-EM structure of 90S small subunit preribosomes in transition states (State C)
Resolution: 8.6 Å
EM Method: Single-particle
Fitted PDBs: 6lqr
Q-score: 0.08
Du Y, An W, Zhu X, Sun Q, Qi J, Ye K
Science (2020) 369 pp. 1477-1481 [ DOI: doi:10.1126/science.aba9690 Pubmed: 32943522 ]
- U3 small nucleolar rna-associated protein 6 (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U3 small nucleolar rna-associated protein 9 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Protein sof1 (56 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 13 kda ribonucleoprotein-associated protein (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U3 small nucleolar rna-associated protein 10 (200 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Net1-associated nuclear protein 1 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U3 small nucleolar rna-associated protein 22 (140 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nucleolar protein 56 (56 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pno1 (36 kDa, Protein from Saccharomyces cerevisiae S288C)
- 18s pre-rrna (582 kDa, RNA from Saccharomyces cerevisiae S288C)
- U3 small nucleolar ribonucleoprotein protein imp4 (33 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 5' ets (225 kDa, RNA from Saccharomyces cerevisiae S288C)
- Ribosome biogenesis protein enp2 (81 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 90s pre-ribosome (dhr1-depleted, state c) (5 MDa, Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U3 small nucleolar rna-associated protein 5 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U3 small nucleolar rna-associated protein 8 (80 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nucleolar protein 58 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s8-a (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Periodic tryptophan protein 2 (104 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Essential nuclear protein 1 (55 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U3 small nucleolar ribonucleoprotein protein lcp5 (40 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U3 small nucleolar rna-associated protein 12 (106 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U3 small nucleolar rna-associated protein 11 (29 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U3 small nucleolar ribonucleoprotein protein imp3 (21 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna cytidine acetyltransferase (119 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Nucleolar complex protein 4 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s4-a (29 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rrna-processing protein fcf2 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U3 small nucleolar rna-associated protein 15 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna 3'-terminal phosphate cyclase-like protein (40 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U3 small nucleolar rna-associated protein 18 (66 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Bud site selection protein 21 (24 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ribosomal rna-processing protein 7 (34 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ribosomal rna-processing protein 9 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s22-b (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s6-a (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U3 small nucleolar rna-associated protein 7 (62 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- U3 small nucleolar rna-associated protein 20 (287 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ribosome biogenesis protein bms1 (135 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ribosomal rna small subunit methyltransferase nep1 (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Protein bfr2 (61 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U3 snorna (106 kDa, RNA from Saccharomyces cerevisiae S288C)
- U3 small nucleolar rna-associated protein 21 (104 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- U3 small nucleolar rna-associated protein 13 (91 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nucleolar complex protein 14 (94 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unassigned helices (29 kDa, Protein from Saccharomyces cerevisiae S288C)
- Rrna 2'-o-methyltransferase fibrillarin (34 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U3 small nucleolar rna-associated protein 4 (87 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Something about silencing protein 10 (70 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rrna biogenesis protein rrp5 (193 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U3 small nucleolar rna-associated protein 14 (103 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rrna-processing protein fcf1 (21 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U3 small nucleolar rna-associated protein mpp10 (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cryo-EM structure of the 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP, state 1)
Resolution: 8.7 Å
EM Method: Single-particle
Fitted PDBs: 5wyj
Q-score: 0.16
Sun Q, Zhu X, Qi J, An W, Lan P, Tan D, Chen R, Wang B, Zheng S, Zhang C, Chen X, Zhang W, Chen J, Dong MQ, Ye K
eLife (2017) 6 [ Pubmed: 28244370 DOI: doi:10.7554/eLife.22086 ]
- Enp2 (60 kDa, Protein from Baker's yeast)
- 90s small subunit pre-ribosome (dhr1-depleted, enp1-tap) (Complex from Saccharomyces cerevisiae)
- 40s ribosomal protein s28-a (7 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s24-a (15 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s5 (25 kDa, Protein from Baker's yeast)
- Rrna biogenesis protein rrp5 (193 kDa, Protein from Baker's yeast)
- U3 small nucleolar ribonucleoprotein protein imp4 (33 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s8-a (22 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s27-a (8 kDa, Protein from Baker's yeast)
- Ribosomal rna small subunit methyltransferase nep1 (27 kDa, Protein from Baker's yeast)
- Nucleolar protein 56 (56 kDa, Protein from Baker's yeast)
- Helical domain protein (137 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s1-a (28 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s11-a (17 kDa, Protein from Baker's yeast)
- Ribosomal rna-processing protein 7 (34 kDa, Protein from Baker's yeast)
- Utp9 (48 kDa, Protein from Baker's yeast)
- Ribosomal rna-processing protein 9 (65 kDa, Protein from Baker's yeast)
- Ubiquitin-40s ribosomal protein s31 (17 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s16-a (15 kDa, Protein from Baker's yeast)
- Essential nuclear protein 1 (55 kDa, Protein from Baker's yeast)
- Rrna-processing protein fcf1 (21 kDa, Protein from Baker's yeast)
- Unassigned helices (87 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 18 (66 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 21 (104 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 22 (140 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 13 (91 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s6-a (27 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s14-a (14 kDa, Protein from Baker's yeast)
- Helical domain protein (84 kDa, Protein from Baker's yeast)
- Utp15 (43 kDa, Protein from Baker's yeast)
- Ribosome biogenesis protein bms1 (135 kDa, Protein from Baker's yeast)
- U3 small nucleolar ribonucleoprotein protein imp3 (21 kDa, Protein from Baker's yeast)
- Mpp10,u3 small nucleolar rna-associated protein mpp10 (54 kDa, Protein from Baker's yeast)
- Utp4 (66 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s22-a (14 kDa, Protein from Baker's yeast)
- Sof1 (41 kDa, Protein from Baker's yeast)
- Rrna 2'-o-methyltransferase fibrillarin (34 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s4-a (29 kDa, Protein from Baker's yeast)
- Ribosome biogenesis protein utp30 (31 kDa, Protein from Baker's yeast)
- Utp7 (47 kDa, Protein from Baker's yeast)
- Utp17 (76 kDa, Protein from Baker's yeast)
- Pre-rrna-processing protein pno1 (30 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 10,utp10 (173 kDa, Protein from Baker's yeast)
- Rna 3'-terminal phosphate cyclase-like protein (40 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s23-a (16 kDa, Protein from Baker's yeast)
- 18s ribosomal rna (583 kDa, RNA from Baker's yeast)
- 13 kda ribonucleoprotein-associated protein (13 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s30-a (7 kDa, Protein from Baker's yeast)
- Utp11 (21 kDa, Protein from Baker's yeast)
- 5ets rna (225 kDa, RNA from Baker's yeast)
- Periodic tryptophan protein 2 (104 kDa, Protein from Baker's yeast)
- Nucleolar protein 58 (57 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s7-a (21 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s12 (15 kDa, Protein from Baker's yeast)
- Utp20 (212 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s9-a (22 kDa, Protein from Baker's yeast)
- U3 rna (106 kDa, RNA from Baker's yeast)
- 40s ribosomal protein s13 (17 kDa, Protein from Baker's yeast)
- Utp8 (60 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 12 (106 kDa, Protein from Baker's yeast)
- Utp5 (54 kDa, Protein from Baker's yeast)
- Krr1 small subunit processome component (37 kDa, Protein from Baker's yeast)