Cryo-EM structure of STING oligomer bound to cGAMP and NVS-STG2
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8flk
Q-score: 0.438
Li J, Canham SM, Wu H, Henault M, Chen L, Liu G, Chen Y, Yu G, Miller HR, Hornak V, Brittain SM, Michaud GA, Tutter A, Broom W, Digan ME, McWhirter SM, Sivick KE, Pham HT, Chen CH, Tria GS, McKenna JM, Schirle M, Mao X, Nicholson TB, Wang Y, Jenkins JL, Jain RK, Tallarico JA, Patel SJ, Zheng L, Ross NT, Cho CY, Zhang X, Bai XC, Feng Y
Nat Chem Biol (2024) 20 pp. 365-372 [ Pubmed: 37828400 DOI: doi:10.1038/s41589-023-01434-y ]
- 4-({[4-(2-tert-butyl-5,5-dimethyl-1,3-dioxan-2-yl)phenyl]methyl}amino)-3-methoxybenzoic acid (427 Da, Ligand)
- Cgamp (674 Da, Ligand)
- Stimulator of interferon genes protein (39 kDa, Protein from Homo sapiens)
- Sting tetramer (300 kDa, Complex from Homo sapiens)
Cryo-EM structure of STING oligomer bound to cGAMP, NVS-STG2 and C53
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8flm
Q-score: 0.573
Li J, Canham SM, Wu H, Henault M, Chen L, Liu G, Chen Y, Yu G, Miller HR, Hornak V, Brittain SM, Michaud GA, Tutter A, Broom W, Digan ME, McWhirter SM, Sivick KE, Pham HT, Chen CH, Tria GS, McKenna JM, Schirle M, Mao X, Nicholson TB, Wang Y, Jenkins JL, Jain RK, Tallarico JA, Patel SJ, Zheng L, Ross NT, Cho CY, Zhang X, Bai XC, Feng Y
Nat Chem Biol (2024) 20 pp. 365-372 [ Pubmed: 37828400 DOI: doi:10.1038/s41589-023-01434-y ]
- 4-({[4-(2-tert-butyl-5,5-dimethyl-1,3-dioxan-2-yl)phenyl]methyl}amino)-3-methoxybenzoic acid (427 Da, Ligand)
- Stimulator of interferon genes protein (39 kDa, Protein from Homo sapiens)
- Sting tetramer (300 kDa, Complex from Homo sapiens)
- Cgamp (674 Da, Ligand)
- 1-[(2-chloro-6-fluorophenyl)methyl]-3,3-dimethyl-2-oxo-n-[(2,4,6-trifluorophenyl)methyl]-2,3-dihydro-1h-indole-6-carboxamide (490 Da, Ligand)
Cryo-EM structure of human cohesin-CTCF-DNA complex
Resolution: 6.5 Å
EM Method: Single-particle
Fitted PDBs: 7w1m
Q-score: 0.163
Zhang H, Shi Z, Banigan EJ, Kim Y, Yu H, Bai XC, Finkelstein IJ
Mol Cell (2023) 83 pp. 2856-2871.e8 [ Pubmed: 37536339 DOI: doi:10.1016/j.molcel.2023.07.006 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (Complex)
- Dna (118-mer) (36 kDa, DNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Cohesin subunit sa-1 (144 kDa, Protein from Homo sapiens)
- Structural maintenance of chromosomes protein 1a (143 kDa, Protein from Homo sapiens)
- Human cohesin-nipbl-ctcf-dna complex (Complex from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Structural maintenance of chromosomes protein 3 (141 kDa, Protein from Homo sapiens)
- Nipped-b-like protein (167 kDa, Protein from Homo sapiens)
- Double-strand-break repair protein rad21 homolog (71 kDa, Protein from Homo sapiens)
- Human cohesin-nipbl-ctcf (Complex)
- Dna (118-mer) (36 kDa, DNA from Homo sapiens)
- Transcriptional repressor ctcf (82 kDa, Protein from Homo sapiens)
Cryo-EM map of octopus sensory receptor CRT1
Resolution: 2.62 Å
EM Method: Single-particle
Fitted PDBs: 8eis
Q-score: 0.574
Kang G, Allard CAH, Valencia-Montoya WA, van Giesen L, Kim JJ, Kilian PB, Bai X, Bellono NW, Hibbs RE
Nature (2023) 616 pp. 378-383 [ Pubmed: 37045917 DOI: doi:10.1038/s41586-023-05808-z ]
- 2-[2-[(1~{s},2~{s},4~{s},5'~{r},6~{r},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol (516 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Octopus sensory receptor crt1 in complex with diosgenin (200 MDa, Complex from Octopus bimaculoides)
- Octopus sensory receptor (43 kDa, Protein from Octopus bimaculoides)
Cryo-EM map of squid sensory receptor CRB1
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 8eiz
Q-score: 0.505
Kang G, Allard CAH, Valencia-Montoya WA, van Giesen L, Kim JJ, Kilian PB, Bai X, Bellono NW, Hibbs RE
Nature (2023) 616 pp. 378-383 [ Pubmed: 37045917 DOI: doi:10.1038/s41586-023-05808-z ]
- Squid sensory receptor crb1 in complex with denatonium (200 MDa, Complex from Sepioloidea lineolata)
- N-benzyl-2-(2,6-dimethylanilino)-n,n-diethyl-2-oxoethan-1-aminium (325 Da, Ligand)
- Squid sensory receptor crb1 (45 kDa, Protein from Sepioloidea lineolata)
- Water (18 Da, Ligand)
Human alpha3 Na+/K+-ATPase in its Na+-occluded state
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8d3u
Q-score: 0.444
Nguyen PT, Deisl C, Fine M, Tippetts TS, Uchikawa E, Bai XC, Levine B
Nat Commun (2022) 13 pp. 5293-5293 [ Pubmed: 36075933 DOI: doi:10.1038/s41467-022-32990-x ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Sodium/potassium-transporting atpase subunit alpha-3 (111 kDa, Protein from Homo sapiens)
- Na+/k+-atpase (Complex from Homo sapiens)
- Fxyd domain-containing ion transport regulator 6 (10 kDa, Protein from Homo sapiens)
- Sodium/potassium-transporting atpase subunit beta-1 (35 kDa, Protein from Homo sapiens)
- Tetrafluoroaluminate ion (102 Da, Ligand)
Human alpha3 Na+/K+-ATPase in its AMPPCP-bound cytoplasmic side-open state
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8d3w
Q-score: 0.493
Nguyen PT, Deisl C, Fine M, Tippetts TS, Uchikawa E, Bai XC, Levine B
Nat Commun (2022) 13 pp. 5293-5293 [ Pubmed: 36075933 DOI: doi:10.1038/s41467-022-32990-x ]
- Sodium/potassium-transporting atpase subunit alpha-3 (111 kDa, Protein from Homo sapiens)
- Na+/k+-atpase (Complex from Homo sapiens)
- Fxyd domain-containing ion transport regulator 6 (10 kDa, Protein from Homo sapiens)
- Phosphomethylphosphonic acid adenylate ester (505 Da, Ligand)
- Sodium/potassium-transporting atpase subunit beta-1 (35 kDa, Protein from Homo sapiens)
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)
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 7sii
Q-score: 0.491
Lu D, Shang G, Li J, Lu Y, Bai XC, Zhang X
Nature (2022) 604 pp. 557-562 [ DOI: doi:10.1038/s41586-022-04559-7 Pubmed: 35388221 ]
- 1-[(2-chloro-6-fluorophenyl)methyl]-3,3-dimethyl-2-oxo-n-[(2,4,6-trifluorophenyl)methyl]-2,3-dihydro-1h-indole-6-carboxamide (490 Da, Ligand)
- Human sting (Complex from Homo sapiens)
- Cgamp (674 Da, Ligand)
- Stimulator of interferon genes protein (39 kDa, Protein from Homo sapiens)