Electron Microscopy Data Bank

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EMD-29560

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5-MeO-DMT-bound serotonin 1A (5-HT1A) receptor-Gi1 protein complex

Release date: May 15, 2024
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 8fy8
Q-score: 0.519

Warren AL, Lankri D, Cunningham MJ, Serrano IC, Parise LF, Kruegel AC, Duggan P, Zilberg G, Capper MJ, Havel V, Russo SJ, Sames D, Wacker D

Nature (2024) 630 pp. 237-246 [ DOI: doi:10.1038/s41586-024-07403-2 Pubmed: 38720072 ]

Sample:

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EMD-29571

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4-F, 5-MeO-PyrT-bound serotonin 1A (5-HT1A) receptor-Gi1 protein complex

Release date: May 15, 2024
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8fye
Q-score: 0.53

Warren AL, Lankri D, Cunningham MJ, Serrano IC, Parise LF, Kruegel AC, Duggan P, Zilberg G, Capper MJ, Havel V, Russo SJ, Sames D, Wacker D

Nature (2024) 630 pp. 237-246 [ Pubmed: 38720072 DOI: doi:10.1038/s41586-024-07403-2 ]

Sample:

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EMD-29585

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Vilazodone-bound serotonin 1A (5-HT1A) receptor-Gi1 protein complex

Release date: May 15, 2024
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 8fyl
Q-score: 0.525

Warren AL, Lankri D, Cunningham MJ, Serrano IC, Parise LF, Kruegel AC, Duggan P, Zilberg G, Capper MJ, Havel V, Russo SJ, Sames D, Wacker D

Nature (2024) 630 pp. 237-246 [ Pubmed: 38720072 DOI: doi:10.1038/s41586-024-07403-2 ]

Sample:

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EMD-29597

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LSD-bound serotonin 1A (5-HT1A) receptor-Gi1 protein complex

Release date: May 15, 2024
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 8fyt
Q-score: 0.544

Warren AL, Lankri D, Cunningham MJ, Serrano IC, Parise LF, Kruegel AC, Duggan P, Zilberg G, Capper MJ, Havel V, Russo SJ, Sames D, Wacker D

Nature (2024) 630 pp. 237-246 [ Pubmed: 38720072 DOI: doi:10.1038/s41586-024-07403-2 ]

Sample:

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EMD-29599

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Buspirone-bound serotonin 1A (5-HT1A) receptor-Gi1 protein complex

Release date: May 15, 2024
Resolution: 2.62 Å
EM Method: Single-particle
Fitted PDBs: 8fyx
Q-score: 0.545

Warren AL, Lankri D, Cunningham MJ, Serrano IC, Parise LF, Kruegel AC, Duggan P, Zilberg G, Capper MJ, Havel V, Russo SJ, Sames D, Wacker D

Nature (2024) 630 pp. 237-246 [ DOI: doi:10.1038/s41586-024-07403-2 Pubmed: 38720072 ]

Sample:

Soluble cytochrome b562,5-hydroxytryptamine receptor 1a,5-hydroxytryptamine receptor 1a (61 kDa, Protein from Homo sapiens)
Buspirone (385 Da, Ligand)
Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (8 kDa, Protein from Homo sapiens)
Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
Cholesterol hemisuccinate (486 Da, Ligand)
[(2r)-1-[oxidanyl-[(2r,3r,5s,6r)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-3-tetradecanoyloxy-propan-2-yl] (5e,8e)-hexadeca-5,8,11,14-tetraenoate (854 Da, Ligand)
Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
Serotonin 1a (5-ht1a) receptor-gi1 protein complex (Complex from Escherichia coli, Homo sapiens)

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EMD-38232

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The cryo-EM structure of the RAD51 L2 loop bound to the linker DNA with the blunt end of the nucleosome

Release date: March 27, 2024
Resolution: 4.36 Å
EM Method: Single-particle
Fitted PDBs: 8xbx
Q-score: 0.072

Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H

Nature (2024) 628 pp. 212-220 [ Pubmed: 38509361 DOI: doi:10.1038/s41586-024-07196-4 ]

Sample:

Dna (5'-d(p*ap*ap*cp*gp*ap*ap*ap*ap*cp*gp*gp*cp*cp*ap*cp*cp*ap*cp*g)-3') (48 kDa, DNA from synthetic construct)
Rad51-nucleosome complex (Complex from Homo sapiens)
Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
Dna (5'-d(p*cp*gp*tp*gp*gp*tp*gp*gp*cp*cp*gp*tp*tp*tp*tp*cp*gp*tp*t)-3') (48 kDa, DNA from Escherichia coli)

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EMD-16563

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80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex

Release date: Sept. 20, 2023
Resolution: 1.97 Å
EM Method: Single-particle
Fitted PDBs: 8ccs
Q-score: 0.64

Milicevic N, Jenner L, Myasnikov A, Yusupov M, Yusupova G

Nature (2024) 625 pp. 393-400 [ Pubmed: 38030725 DOI: doi:10.1038/s41586-023-06780-4 ]

Sample:

40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae)
Transfer rna phe (24 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
Transfer rna fmet (24 kDa, RNA from Escherichia coli)
40s ribosomal protein s26 (13 kDa, Protein from Saccharomyces cerevisiae)
Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s17-a (15 kDa, Protein from Saccharomyces cerevisiae)
Messenger rna (12 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae)
60s acidic ribosomal protein p0 (33 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
Water (18 Da, Ligand)
60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
25s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l39 (6 kDa, Protein from Saccharomyces cerevisiae)
Potassium ion (39 Da, Ligand)
60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
Hlj1_g0030400.mrna.1.cds.1 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
Elongating saccharomyces cerevisiae 80s ribosome in complex with ligands (Complex from Saccharomyces cerevisiae)
60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s6-a (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l11-a (19 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae)
Rps3 isoform 1 (26 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s8-b (22 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s4-a (29 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l12-a (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae)
5.8s ribosomal rna (50 kDa, RNA from Saccharomyces cerevisiae)
40s ribosomal protein s10-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae)
Magnesium ion (24 Da, Ligand)
40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae)
5s ribosomal rna (38 kDa, RNA from Saccharomyces cerevisiae)
40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
Ubiquitin-40s ribosomal protein s31 (17 kDa, Protein from Saccharomyces cerevisiae)
18s ribosomal rna (580 kDa, RNA from Saccharomyces cerevisiae)
40s ribosomal protein s15 (16 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae)
Di-peptide (296 Da, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l41-a (3 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae)
Spermidine (145 Da, Ligand)
40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)

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EMD-16591

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80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex

Release date: Sept. 20, 2023
Resolution: 2.72 Å
EM Method: Single-particle
Fitted PDBs: 8cdl
Q-score: 0.533

Milicevic N, Jenner L, Myasnikov A, Yusupov M, Yusupova G

Nature (2024) 625 pp. 393-400 [ Pubmed: 38030725 DOI: doi:10.1038/s41586-023-06780-4 ]

Sample:

40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae)
Transfer rna phe (24 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
Transfer rna fmet (24 kDa, RNA from Escherichia coli)
40s ribosomal protein s26 (13 kDa, Protein from Saccharomyces cerevisiae)
Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s17-a (15 kDa, Protein from Saccharomyces cerevisiae)
Messenger rna (12 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae)
60s acidic ribosomal protein p0 (33 kDa, Protein from Saccharomyces cerevisiae)
Dipeptide (296 Da, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
Water (18 Da, Ligand)
60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
25s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l39 (6 kDa, Protein from Saccharomyces cerevisiae)
Potassium ion (39 Da, Ligand)
60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
Hlj1_g0030400.mrna.1.cds.1 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
Elongating saccharomyces cerevisiae 80s ribosome in complex with ligands (Complex from Saccharomyces cerevisiae)
60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s6-a (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l11-a (19 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae)
Rps3 isoform 1 (26 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s8-b (22 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s4-a (29 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l12-a (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae)
5.8s ribosomal rna (50 kDa, RNA from Saccharomyces cerevisiae)
40s ribosomal protein s10-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l23-a (13 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae)
Magnesium ion (24 Da, Ligand)
40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae)
5s ribosomal rna (38 kDa, RNA from Saccharomyces cerevisiae)
40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
Ubiquitin-40s ribosomal protein s31 (17 kDa, Protein from Saccharomyces cerevisiae)
18s ribosomal rna (580 kDa, RNA from Saccharomyces cerevisiae)
40s ribosomal protein s15 (16 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l41-a (3 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae)
Spermidine (145 Da, Ligand)
40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)

[Show more]

EMD-16594

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Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin

Release date: Sept. 20, 2023
Resolution: 2.04 Å
EM Method: Single-particle
Fitted PDBs: 8cdr
Q-score: 0.615

Milicevic N, Jenner L, Myasnikov A, Yusupov M, Yusupova G

Nature (2024) 625 pp. 393-400 [ Pubmed: 38030725 DOI: doi:10.1038/s41586-023-06780-4 ]

Sample:

40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae)
Transfer rna phe (24 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
Transfer rna fmet (24 kDa, RNA from Escherichia coli)
40s ribosomal protein s26 (13 kDa, Protein from Saccharomyces cerevisiae)
Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s17-a (15 kDa, Protein from Saccharomyces cerevisiae)
Messenger rna (12 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae)
60s acidic ribosomal protein p0 (33 kDa, Protein from Saccharomyces cerevisiae)
Dipeptide (296 Da, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
Water (18 Da, Ligand)
60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
25s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
[1r-(1.alpha.,3a.beta.,4.beta.,4a.beta.,7.beta.,7a.alpha.,8a.beta.)]8a-[(6-deoxy-4-o-methyl-beta-d-altropyranosyloxy)methyl]-4-formyl-4,4a,5,6,7,7a,8,8a-octahydro-7-methyl-3-(1-methylethyl)-1,4-methano-s-indacene-3a(1h)-carboxylic acid (494 Da, Ligand)
40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l39 (6 kDa, Protein from Saccharomyces cerevisiae)
Guanosine-5'-diphosphate (443 Da, Ligand)
Potassium ion (39 Da, Ligand)
60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
Hlj1_g0030400.mrna.1.cds.1 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s6-a (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l11-a (19 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae)
Rps3 isoform 1 (26 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s8-b (22 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s4-a (29 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l12-a (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae)
80s saccharomyces cerevisiae ribosome in complex with eef2.sordarin and ligands (Complex from Saccharomyces cerevisiae)
5.8s ribosomal rna (50 kDa, RNA from Saccharomyces cerevisiae)
40s ribosomal protein s10-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae)
Magnesium ion (24 Da, Ligand)
40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae)
5s ribosomal rna (38 kDa, RNA from Saccharomyces cerevisiae)
40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
Ubiquitin-40s ribosomal protein s31 (17 kDa, Protein from Saccharomyces cerevisiae)
18s ribosomal rna (580 kDa, RNA from Saccharomyces cerevisiae)
40s ribosomal protein s15 (16 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l41-a (3 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae)
Spermidine (145 Da, Ligand)
40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae)
Elongation factor 2 (93 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)

[Show more]

EMD-16609

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Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin

Release date: Sept. 20, 2023
Resolution: 2.05 Å
EM Method: Single-particle
Fitted PDBs: 8ceh
Q-score: 0.617

Milicevic N, Jenner L, Myasnikov A, Yusupov M, Yusupova G

Nature (2024) 625 pp. 393-400 [ Pubmed: 38030725 DOI: doi:10.1038/s41586-023-06780-4 ]

Sample:

Elongation factor 2 (93 kDa, Protein from Saccharomyces cerevisiae)
[1r-(1.alpha.,3a.beta.,4.beta.,4a.beta.,7.beta.,7a.alpha.,8a.beta.)]8a-[(6-deoxy-4-o-methyl-beta-d-altropyranosyloxy)methyl]-4-formyl-4,4a,5,6,7,7a,8,8a-octahydro-7-methyl-3-(1-methylethyl)-1,4-methano-s-indacene-3a(1h)-carboxylic acid (494 Da, Ligand)
60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
Polypeptide (296 Da, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l39 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae)
Guanosine-5'-diphosphate (443 Da, Ligand)
Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae)
5.8s ribosomal rna (50 kDa, RNA from Saccharomyces cerevisiae)
Hlj1_g0030400.mrna.1.cds.1 (6 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae)
Rps3 isoform 1 (26 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s26 (13 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae)
80s saccharomyces cerevisiae ribosome in complex with eef2.sordarin and ligands (Complex from Saccharomyces cerevisiae)
60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae)
Spermidine (145 Da, Ligand)
60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
5s ribosomal rna (38 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
Ubiquitin-40s ribosomal protein s31 (17 kDa, Protein from Saccharomyces cerevisiae)
Transfer rna phe (24 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s17-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
Potassium ion (39 Da, Ligand)
40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s10-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s4-a (29 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l11-a (19 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
Phosphate ion (94 Da, Ligand)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l41 (3 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s15 (16 kDa, Protein from Saccharomyces cerevisiae)
Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
Water (18 Da, Ligand)
40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
60s acidic ribosomal protein p0 (33 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s8-b (22 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae)
18s ribosomal rna (580 kDa, RNA from Saccharomyces cerevisiae)
Messenger rna (12 kDa, RNA from Saccharomyces cerevisiae)
Transfer rna fmet (24 kDa, RNA from Escherichia coli)
60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
Rpl9a isoform 1 (21 kDa, Protein from Saccharomyces cerevisiae)
25s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s6-a (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l12-a (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)

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