Structure of ribosomal complex bound with Rbg1/Tma46
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 7rr5
Q-score: 0.437
Zeng F, Li X, Pires-Alves M, Chen X, Hawk CW, Jin H
Cell Rep (2021) 37 pp. 109877-109877 [ Pubmed: 34706231 DOI: doi:10.1016/j.celrep.2021.109877 ]
- Ubiquitin-40s ribosomal protein s31 (17 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l21-a (18 kDa, Protein from Baker's yeast)
- A-trna (Complex from Saccharomyces cerevisiae)
- 60s ribosomal protein l39 (6 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s13 (17 kDa, Protein from Baker's yeast)
- Rps15 isoform 1 (16 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l42-a (12 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l2-b (27 kDa, Protein from Baker's yeast)
- Rps22a isoform 1 (14 kDa, Protein from Baker's yeast)
- Rpp0 isoform 1 (33 kDa, Protein from Baker's yeast)
- Rpl12a isoform 1 (17 kDa, Protein from Baker's yeast)
- Rps25a isoform 1 (12 kDa, Protein from Baker's yeast)
- 5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l14-a (15 kDa, Protein from Baker's yeast)
- Rps2 isoform 1 (27 kDa, Protein from Baker's yeast)
- Rbg1/tma46 (Complex from Saccharomyces cerevisiae)
- 60s ribosomal protein l25 (15 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s27-a (8 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l15-a (24 kDa, Protein from Baker's yeast)
- 5s rrna (38 kDa, RNA from Saccharomyces cerevisiae)
- Eif5a (Complex from Saccharomyces cerevisiae)
- Rps26b isoform 1 (13 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l34-a (13 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s17-a (15 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l23-b (14 kDa, Protein from Baker's yeast)
- Aspartic acid (133 Da, Ligand)
- Rpl3 isoform 1 (43 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l28 (16 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l33-a (12 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s0 (28 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l22-a (13 kDa, Protein from Baker's yeast)
- 60s subunit (Complex from Saccharomyces cerevisiae)
- Rps8a isoform 1 (22 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l43-a (10 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s4 (29 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l20-a (20 kDa, Protein from Baker's yeast)
- Rpl10 isoform 1 (25 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s12 (15 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l1 (17 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l16-a (22 kDa, Protein from Baker's yeast)
- Rps3 isoform 1 (26 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s30 (7 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s16-a (15 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s18-b (17 kDa, Protein from Baker's yeast)
- Mrna (Complex from Saccharomyces cerevisiae)
- Rpl24a isoform 1 (17 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l19-a (21 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l6 (20 kDa, Protein from Baker's yeast)
- Translation machinery-associated protein 46 (39 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s11-b (17 kDa, Protein from Baker's yeast)
- Eukaryotic translation initiation factor 5a (17 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s14-b (14 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s23 (16 kDa, Protein from Baker's yeast)
- Rpl4a isoform 1 (39 kDa, Protein from Baker's yeast)
- Rps20 isoform 1 (13 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s21-a (9 kDa, Protein from Baker's yeast)
- Ribosomal protein l37 (9 kDa, Protein from Baker's yeast)
- 18s rrna (579 kDa, RNA from Saccharomyces cerevisiae)
- Rpl5 isoform 1 (33 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l9-a (21 kDa, Protein from Baker's yeast)
- Mrna (5 kDa, RNA from Saccharomyces cerevisiae)
- A-trna (24 kDa, RNA from Saccharomyces cerevisiae)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l13 (22 kDa, Protein from Baker's yeast)
- Magnesium ion (24 Da, Ligand)
- Rps5p (25 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l27 (15 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l18-b (20 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l8-a (28 kDa, Protein from Baker's yeast)
- 40s subunit (Complex from Saccharomyces cerevisiae)
- Rpl29 isoform 1 (6 kDa, Protein from Baker's yeast)
- Rpl11b isoform 1 (19 kDa, Protein from Baker's yeast)
- P-trna (Complex from Saccharomyces cerevisiae)
- 25s rrna (1 MDa, RNA from Saccharomyces cerevisiae)
- Rpl38 isoform 1 (8 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l26-a (14 kDa, Protein from Baker's yeast)
- Rpl32 isoform 1 (14 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l17-a (20 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l31-a (12 kDa, Protein from Baker's yeast)
- Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Baker's yeast)
- Ribosomal complex with rbg1/tma46 (Complex from Saccharomyces cerevisiae)
- 60s ribosomal protein l7-a (27 kDa, Protein from Baker's yeast)
- Ribosome-interacting gtpase 1 (45 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- P-trna (24 kDa, RNA from Saccharomyces cerevisiae)
- 40s ribosomal protein s9-a (22 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s6 (27 kDa, Protein from Baker's yeast)
- Rps1a isoform 1 (28 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l35-a (13 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l30 (11 kDa, Protein from Baker's yeast)
- Rps29a isoform 1 (6 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l41-a (3 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s24 (15 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s10-a (12 kDa, Protein from Baker's yeast)
- Rps28a isoform 1 (7 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s7 (21 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s19-a (15 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l36-a (11 kDa, Protein from Baker's yeast)
Apo spike protein of SARS-CoV2
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 7dzw
Q-score: 0.206
Liu Y, Soh WT, Kishikawa JI, Hirose M, Nakayama EE, Li S, Sasai M, Suzuki T, Tada A, Arakawa A, Matsuoka S, Akamatsu K, Matsuda M, Ono C, Torii S, Kishida K, Jin H, Nakai W, Arase N, Nakagawa A, Matsumoto M, Nakazaki Y, Shindo Y, Kohyama M, Tomii K, Ohmura K, Ohshima S, Okamoto T, Yamamoto M, Nakagami H, Matsuura Y, Nakagawa A, Kato T, Okada M, Standley DM, Shioda T, Arase H
Cell (2021) 184 pp. 3452-3466.e18 [ DOI: doi:10.1016/j.cell.2021.05.032 Pubmed: 34139176 ]
SARS-CoV2 spike protein with Fab fragment of enhancing antibody 8D2
Liu Y, Soh WT, Kishikawa JI, Hirose M, Nakayama EE, Li S, Sasai M, Suzuki T, Tada A, Arakawa A, Matsuoka S, Akamatsu K, Matsuda M, Ono C, Torii S, Kishida K, Jin H, Nakai W, Arase N, Nakagawa A, Matsumoto M, Nakazaki Y, Shindo Y, Kohyama M, Tomii K, Ohmura K, Ohshima S, Okamoto T, Yamamoto M, Nakagami H, Matsuura Y, Nakagawa A, Kato T, Okada M, Standley DM, Shioda T, Arase H
Cell (2021) 184 pp. 3452-3466.e18 [ DOI: doi:10.1016/j.cell.2021.05.032 Pubmed: 34139176 ]
SARS-CoV2 spike protein with Fab fragment of enhancing antibody (8D2)-1
Liu Y, Soh WT, Kishikawa JI, Hirose M, Nakayama EE, Li S, Sasai M, Suzuki T, Tada A, Arakawa A, Matsuoka S, Akamatsu K, Matsuda M, Ono C, Torii S, Kishida K, Jin H, Nakai W, Arase N, Nakagawa A, Matsumoto M, Nakazaki Y, Shindo Y, Kohyama M, Tomii K, Ohmura K, Ohshima S, Okamoto T, Yamamoto M, Nakagami H, Matsuura Y, Nakagawa A, Kato T, Okada M, Standley DM, Shioda T, Arase H
Cell (2021) 184 pp. 3452-3466.e18 [ DOI: doi:10.1016/j.cell.2021.05.032 Pubmed: 34139176 ]
SARS-CoV2 spike protein with Fab fragment of enhancing antibody (8D2)-2
Resolution: 3.82 Å
EM Method: Single-particle
Fitted PDBs: 7dzx
Q-score: 0.22
Liu Y, Soh WT, Kishikawa JI, Hirose M, Nakayama EE, Li S, Sasai M, Suzuki T, Tada A, Arakawa A, Matsuoka S, Akamatsu K, Matsuda M, Ono C, Torii S, Kishida K, Jin H, Nakai W, Arase N, Nakagawa A, Matsumoto M, Nakazaki Y, Shindo Y, Kohyama M, Tomii K, Ohmura K, Ohshima S, Okamoto T, Yamamoto M, Nakagami H, Matsuura Y, Nakagawa A, Kato T, Okada M, Standley DM, Shioda T, Arase H
Cell (2021) 184 pp. 3452-3466.e18 [ DOI: doi:10.1016/j.cell.2021.05.032 Pubmed: 34139176 ]
SARS-CoV2 spike protein with Fab fragment of enhancing antibody (8D2)-3
Liu Y, Soh WT, Kishikawa JI, Hirose M, Nakayama EE, Li S, Sasai M, Suzuki T, Tada A, Arakawa A, Matsuoka S, Akamatsu K, Matsuda M, Ono C, Torii S, Kishida K, Jin H, Nakai W, Arase N, Nakagawa A, Matsumoto M, Nakazaki Y, Shindo Y, Kohyama M, Tomii K, Ohmura K, Ohshima S, Okamoto T, Yamamoto M, Nakagami H, Matsuura Y, Nakagawa A, Kato T, Okada M, Standley DM, Shioda T, Arase H
Cell (2021) 184 pp. 3452-3466.e18 [ DOI: doi:10.1016/j.cell.2021.05.032 Pubmed: 34139176 ]
SARS-CoV2 spike protein with Fab fragment of enhancing antibody (8D2)-4
Liu Y, Soh WT, Kishikawa JI, Hirose M, Nakayama EE, Li S, Sasai M, Suzuki T, Tada A, Arakawa A, Matsuoka S, Akamatsu K, Matsuda M, Ono C, Torii S, Kishida K, Jin H, Nakai W, Arase N, Nakagawa A, Matsumoto M, Nakazaki Y, Shindo Y, Kohyama M, Tomii K, Ohmura K, Ohshima S, Okamoto T, Yamamoto M, Nakagami H, Matsuura Y, Nakagawa A, Kato T, Okada M, Standley DM, Shioda T, Arase H
Cell (2021) 184 pp. 3452-3466.e18 [ DOI: doi:10.1016/j.cell.2021.05.032 Pubmed: 34139176 ]
SARS-CoV2 spike protein with Fab fragment of enhancing antibody (2940)-1
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7dzy
Q-score: -0.01
Liu Y, Soh WT, Kishikawa JI, Hirose M, Nakayama EE, Li S, Sasai M, Suzuki T, Tada A, Arakawa A, Matsuoka S, Akamatsu K, Matsuda M, Ono C, Torii S, Kishida K, Jin H, Nakai W, Arase N, Nakagawa A, Matsumoto M, Nakazaki Y, Shindo Y, Kohyama M, Tomii K, Ohmura K, Ohshima S, Okamoto T, Yamamoto M, Nakagami H, Matsuura Y, Nakagawa A, Kato T, Okada M, Standley DM, Shioda T, Arase H
Cell (2021) 184 pp. 3452-3466.e18 [ DOI: doi:10.1016/j.cell.2021.05.032 Pubmed: 34139176 ]
SARS-CoV2 spike protein with Fab fragment of enhancing antibody (2940)-2
Liu Y, Soh WT, Kishikawa JI, Hirose M, Nakayama EE, Li S, Sasai M, Suzuki T, Tada A, Arakawa A, Matsuoka S, Akamatsu K, Matsuda M, Ono C, Torii S, Kishida K, Jin H, Nakai W, Arase N, Nakagawa A, Matsumoto M, Nakazaki Y, Shindo Y, Kohyama M, Tomii K, Ohmura K, Ohshima S, Okamoto T, Yamamoto M, Nakagami H, Matsuura Y, Nakagawa A, Kato T, Okada M, Standley DM, Shioda T, Arase H
Cell (2021) 184 pp. 3452-3466.e18 [ DOI: doi:10.1016/j.cell.2021.05.032 Pubmed: 34139176 ]
Capsid structure of a freshwater cyanophage Siphoviridae Mic1
Resolution: 3.53 Å
EM Method: Single-particle
Fitted PDBs: 6j3q
Q-score: 0.502
Jin H, Jiang YL, Yang F, Zhang JT, Li WF, Zhou K, Ju J, Chen Y, Zhou CZ
Structure (2019) 27 pp. 1508- [ DOI: doi:10.1016/j.str.2019.07.003 Pubmed: 31378451 ]
- Cement protein (10 kDa, Protein from Microcystis phage Mic1)
- Major capsid protein (37 kDa, Protein from Microcystis phage Mic1)
- Microcystis phage mic1 (Virus from Microcystis phage Mic1)