Molecular mechanism of the the wake-promoting agent TAK-925
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7sr8
Q-score: 0.457
Yin J, Kang Y, McGrath AP, Chapman K, Sjodt M, Kimura E, Okabe A, Koike T, Miyanohana Y, Shimizu Y, Rallabandi R, Lian P, Bai X, Flinspach M, De Brabander JK, Rosenbaum DM
Nat Commun (2022) 13 pp. 2902-2902 [ Pubmed: 35614071 DOI: doi:10.1038/s41467-022-30601-3 ]
- A modified guanine nucleotide-binding protein g(q) subunit alpha (27 kDa, Protein from Homo sapiens)
- Scfv16 (27 kDa, Protein from Homo sapiens)
- Oleic acid (282 Da, Ligand)
- Human orexin receptor 2 - g protein complex (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Hypocretin receptor type 2 (46 kDa, Protein from Homo sapiens)
- Methyl (2r,3s)-3-[(methanesulfonyl)amino]-2-({[(1s,4s)-4-phenylcyclohexyl]oxy}methyl)piperidine-1-carboxylate (424 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (9 kDa, Protein from Homo sapiens)
Structure of the orexin-2 receptor (OX2R) bound to TAK-925, Gi and scFv16
Resolution: 3.17 Å
EM Method: Single-particle
Fitted PDBs: 7sqo
Q-score: 0.487
Yin J, Kang Y, McGrath AP, Chapman K, Sjodt M, Kimura E, Okabe A, Koike T, Miyanohana Y, Shimizu Y, Rallabandi R, Lian P, Bai X, Flinspach M, De Brabander JK, Rosenbaum DM
Nat Commun (2022) 13 pp. 2902-2902 [ Pubmed: 35614071 DOI: doi:10.1038/s41467-022-30601-3 ]
- Orexin receptor type 2 (Complex from Homo sapiens)
- Human ox2r in complex with gai/gb/gg-scfv16. (Complex)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Oleic acid (282 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Bos taurus)
- Scfv-16 (26 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (Complex from Homo sapiens)
- Methyl (2r,3s)-3-[(methanesulfonyl)amino]-2-({[(1s,4s)-4-phenylcyclohexyl]oxy}methyl)piperidine-1-carboxylate (424 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Orexin receptor type 2 (50 kDa, Protein from Homo sapiens)
- Scfv-16 (Complex from synthetic construct)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1, guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (Complex from Bos taurus)
Structure of a spliceosome remodeled for exon ligation
Resolution: 3.85 Å
EM Method: Single-particle
Fitted PDBs: 5mps
Q-score: 0.356
Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ, Nagai K
Nature (2017) 542 pp. 377-380 [ DOI: doi:10.1038/nature21078 Pubmed: 28076345 ]
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
- Ubc4 gene exon (6 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slu7 (44 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cef1 (67 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 18 (28 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Saccharomyces cerevisiae)
- Yeast ubc4 gene for ubiquitin-conjugating enzyme (30 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
- U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae)
- Potassium ion (39 Da, Ligand)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Unknown (5 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor clf1 (82 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae)
- U5 snrna (57 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-processing factor 17 (52 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
- Inositol hexakisphosphate (660 Da, Ligand)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Saccharomyces cerevisiae strain t.52_2h chromosome xii sequence (35 kDa, RNA from Saccharomyces cerevisiae)
- Saccharomyces cerevisiae spliceosome. complex c just after prp16-mediated remodeling (Complex)
- Pre-mrna-splicing factor syf1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
Structure of a spliceosome remodeled for exon ligation
Resolution: 4.17 Å
EM Method: Single-particle
Fitted PDBs: 5mq0
Q-score: 0.223
Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ, Nagai K
Nature (2017) 542 pp. 377-380 [ DOI: doi:10.1038/nature21078 Pubmed: 28076345 ]
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slu7 (44 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cef1 (67 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 18 (28 kDa, Protein from Saccharomyces cerevisiae)
- Unknown protein (5 kDa, Protein from Saccharomyces cerevisiae)
- Saccharomyces cerevisiae strain wi_c_mbsp_4 chromosome vii sequence (57 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Saccharomyces cerevisiae)
- Yeast ubc4 gene for ubiquitin-conjugating enzyme (30 kDa, RNA from Saccharomyces cerevisiae)
- U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae)
- U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
- 3'-exon of ubc4 pre-mrna, bound by prp22 helicase (873 Da, RNA from Saccharomyces cerevisiae)
- Potassium ion (39 Da, Ligand)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor clf1 (82 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snt309 (20 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-processing factor 19 (56 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-processing factor 17 (52 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor atp-dependent rna helicase prp22 (130 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
- Inositol hexakisphosphate (660 Da, Ligand)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Saccharomyces cerevisiae strain t.52_2h chromosome xii sequence (35 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor syf1,pre-mrna-splicing factor syf1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Saccharomyces cerevisiae spliceosome. complex c just after prp16-mediated remodeling (Complex)
- S.cerevisiae chromosome ii reading frame orf ybr230c (376 kDa, RNA from Saccharomyces cerevisiae)
- 5'-exon of ubc4 pre-mrna (6 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 5gam
Q-score: 0.363
Nguyen THD, Galej WP, Bai XC, Oubridge C, Scheres SHW, Newman AJ, Nagai K
Nature (2016) 530 pp. 298-302 [ DOI: doi:10.1038/nature16940 Pubmed: 26829225 ]
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
- U6 snrna, 5' end (9 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
- Unknown polypeptide (1 kDa, Protein from Saccharomyces cerevisiae)
- Foot region of the yeast spliceosomal u4/u6.u5 tri-snrnp (350 kDa, Complex from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 8 (85 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
- U5 snrna (57 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 5gan
Q-score: 0.254
Nguyen TH, Galej WP, Bai XC, Oubridge C, Newman AJ, Scheres SH, Nagai K
Nature (2016) 530 pp. 298-302 [ DOI: doi:10.1038/nature16940 Pubmed: 26829225 ]
- Pre-mrna-splicing factor 6 (104 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
- U6 snrna-associated sm-like protein lsm7 (13 kDa, Protein from Saccharomyces cerevisiae)
- U5 snrna (68 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
- U4/u6 small nuclear ribonucleoprotein prp3 (55 kDa, Protein from Saccharomyces cerevisiae)
- U6 snrna (35 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-processing factor 31 (56 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- U4/u6 small nuclear ribonucleoprotein prp4 (52 kDa, Protein from Saccharomyces cerevisiae)
- Unknown protein (8 kDa, Protein from Saccharomyces cerevisiae)
- U6 snrna-associated sm-like protein lsm6 (9 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing helicase brr2 (246 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
- 13 kda ribonucleoprotein-associated protein (13 kDa, Protein from Saccharomyces cerevisiae)
- Spliceosomal protein dib1 (16 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
- U6 snrna-associated sm-like protein lsm3 (10 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae)
- Snu66 (28 kDa, Protein from Saccharomyces cerevisiae)
- U6 snrna-associated sm-like protein lsm4 (21 kDa, Protein from Saccharomyces cerevisiae)
- U6 snrna-associated sm-like protein lsm8 (12 kDa, Protein from Saccharomyces cerevisiae)
- The overall structure of the yeast spliceosomal u4/u6.u5 tri-snrnp (1 MDa, Complex from Saccharomyces cerevisiae)
- U4 snrna (51 kDa, RNA from Saccharomyces cerevisiae)
- U6 snrna-associated sm-like protein lsm5 (10 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
- U6 snrna-associated sm-like protein lsm2 (11 kDa, Protein from Saccharomyces cerevisiae)
Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 5gao
Q-score: 0.305
Nguyen TH, Galej WP, Bai XC, Oubridge C, Newman AJ, Scheres SH, Nagai K
Nature (2016) 530 pp. 298-302 [ DOI: doi:10.1038/nature16940 Pubmed: 26829225 ]
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
- Snu66 (25 kDa, Protein from Saccharomyces cerevisiae)
- Saccharomyces cerevisiae strain uoa_m2 chromosome 5 sequence (30 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 8 (30 kDa, Protein from Saccharomyces cerevisiae)
- Head region of the yeast spliceosomal u4/u6.u5 tri-snrnp (400 kDa, Complex from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing helicase brr2 (246 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
Body region of the U4/U6.U5 tri-snRNP
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 5gap
Q-score: 0.397
Nguyen TH, Galej WP, Bai XC, Oubridge C, Newman AJ, Scheres SH, Nagai K
Nature (2016) 530 pp. 298-302 [ DOI: doi:10.1038/nature16940 Pubmed: 26829225 ]
- Pre-mrna-splicing factor 6 (104 kDa, Protein from Saccharomyces cerevisiae)
- Unknown protein (6 kDa, Protein from Saccharomyces cerevisiae)
- U4 snrna, 5' region, nucleotides 1-67 (21 kDa, RNA from Saccharomyces cerevisiae)
- U4/u6 small nuclear ribonucleoprotein prp3 (55 kDa, Protein from Saccharomyces cerevisiae)
- 13 kda ribonucleoprotein-associated protein (13 kDa, Protein from Saccharomyces cerevisiae)
- U6 snrna (35 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-processing factor 31 (56 kDa, Protein from Saccharomyces cerevisiae)
- Spliceosomal protein dib1 (16 kDa, Protein from Saccharomyces cerevisiae)
- U4/u6 small nuclear ribonucleoprotein prp4 (52 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae)
- Body region of the u4/u6.u5 tri-snrnp complex (500 kDa, Complex from Saccharomyces cerevisiae)
- Pre-mrna-splicing helicase brr2 (246 kDa, Protein from Saccharomyces cerevisiae)
- U5 snrna (68 kDa, RNA from Saccharomyces cerevisiae)