Cryo-EM structure of the mouse TRPM8 channel in complex with PI(4,5)P2 and Ca2+
Yin Y, Park CG, Zhang F, G Fedor J, Feng S, Suo Y, Im W, Lee SY
Sci Adv (2024) 10 pp. eadp2211-eadp2211 [ Pubmed: 39093967 DOI: doi:10.1126/sciadv.adp2211 ]
- Transient receptor potential cation channel subfamily m member 8 (Complex from Mus musculus)
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Transient receptor potential cation channel subfamily m member 8 (131 kDa, Protein from Mus musculus)
Cryo-EM structure of MraY in complex with analogue 2
Resolution: 2.88 Å
EM Method: Single-particle
Fitted PDBs: 9b70
Q-score: 0.561
Yamamoto K, Sato T, Hao A, Asao K, Kaguchi R, Kusaka S, Ruddarraju RR, Kazamori D, Seo K, Takahashi S, Horiuchi M, Yokota SI, Lee SY, Ichikawa S
Nat Commun (2024) 15 pp. 5085-5085 [ DOI: doi:10.1038/s41467-024-49484-7 Pubmed: 38877016 ]
- Phospho-n-acetylmuramoyl-pentapeptide-transferase (40 kDa, Protein from Aquifex aeolicus VF5)
- (2~{s},3~{s})-3-[(2~{s},3~{r},4~{s},5~{r})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-2-[[3-[[[(2~{s})-6-azanyl-2-(hexadecanoylamino)hexanoyl]amino]methyl]phenyl]methylamino]-3-[(2~{s},3~{s},4~{r},5~{r})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]propanoic acid (934 Da, Ligand)
- Mrayaa nanobody (15 kDa, Protein from Lama glama)
- Complex of mray aa dimer with nanobody bound (200 kDa, Complex from Aquifex aeolicus VF5)
- Water (18 Da, Ligand)
Cryo-EM structure of MraY in complex with analogue 3
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9b71
Q-score: 0.585
Yamamoto K, Sato T, Hao A, Asao K, Kaguchi R, Kusaka S, Ruddarraju RR, Kazamori D, Seo K, Takahashi S, Horiuchi M, Yokota SI, Lee SY, Ichikawa S
Nat Commun (2024) 15 pp. 5085-5085 [ DOI: doi:10.1038/s41467-024-49484-7 Pubmed: 38877016 ]
- Phospho-n-acetylmuramoyl-pentapeptide-transferase (40 kDa, Protein from Aquifex aeolicus VF5)
- Mrayaa nanobody (15 kDa, Protein from Lama glama)
- Complex of mray aa dimer with nanobody bound (200 kDa, Complex from Aquifex aeolicus VF5)
- (2~{s},3~{s})-3-[(2~{s},3~{r},4~{s},5~{r})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-3-[(2~{s},3~{s},4~{r},5~{r})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]-2-[[4-[[[(2~{s})-5-carbamimidamido-2-(hexadecanoylamino)pentanoyl]amino]methyl]phenyl]methylamino]propanoic acid (962 Da, Ligand)
- Water (18 Da, Ligand)
The open state mouse TRPM8 structure in complex with the cooling agonist C3, AITC, and PI(4,5)P2
Resolution: 3.32 Å
EM Method: Single-particle
Fitted PDBs: 8e4l
Q-score: 0.407
Yin Y, Zhang F, Feng S, Butay KJ, Borgnia MJ, Im W, Lee SY
Science (2022) 378 pp. eadd1268-eadd1268 [ DOI: doi:10.1126/science.add1268 Pubmed: 36227998 ]
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Transient receptor potential cation channel subfamily m member 8 (Complex from Mus musculus)
- Nonyl(oxo)di(propan-2-yl)-lambda~5~-phosphane (260 Da, Ligand)
- 3-isothiocyanatoprop-1-ene (99 Da, Ligand)
- Transient receptor potential cation channel subfamily m member 8 (131 kDa, Protein from Mus musculus)
The intermediate C2-state mouse TRPM8 structure in complex with the cooling agonist C3 and PI(4,5)P2
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 8e4m
Q-score: 0.384
Yin Y, Zhang F, Feng S, Butay KJ, Borgnia MJ, Im W, Lee SY
Science (2022) 378 pp. eadd1268-eadd1268 [ DOI: doi:10.1126/science.add1268 Pubmed: 36227998 ]
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Transient receptor potential cation channel subfamily m member 8 (Complex from Mus musculus)
- Nonyl(oxo)di(propan-2-yl)-lambda~5~-phosphane (260 Da, Ligand)
- Transient receptor potential cation channel subfamily m member 8 (131 kDa, Protein from Mus musculus)
The closed C1-state mouse TRPM8 structure in complex with PI(4,5)P2
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 8e4n
Q-score: 0.436
Yin Y, Zhang F, Feng S, Butay KJ, Borgnia MJ, Im W, Lee SY
Science (2022) 378 pp. eadd1268-eadd1268 [ DOI: doi:10.1126/science.add1268 Pubmed: 36227998 ]
- Transient receptor potential cation channel subfamily m member 8 (Complex from Mus musculus)
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
- Transient receptor potential cation channel subfamily m member 8 (131 kDa, Protein from Mus musculus)
The closed C1-state mouse TRPM8 structure in complex with putative PI(4,5)P2
Resolution: 3.43 Å
EM Method: Single-particle
Fitted PDBs: 8e4o
Q-score: 0.425
Yin Y, Zhang F, Feng S, Butay KJ, Borgnia MJ, Im W, Lee SY
Science (2022) 378 pp. eadd1268-eadd1268 [ DOI: doi:10.1126/science.add1268 Pubmed: 36227998 ]
- Transient receptor potential cation channel subfamily m member 8 (Complex from Mus musculus)
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
- Transient receptor potential cation channel subfamily m member 8 (131 kDa, Protein from Mus musculus)
The closed C0-state flycatcher TRPM8 structure in complex with PI(4,5)P2
Resolution: 3.51 Å
EM Method: Single-particle
Fitted PDBs: 8e4q
Q-score: 0.451
Yin Y, Zhang F, Feng S, Butay KJ, Borgnia MJ, Im W, Lee SY
Science (2022) 378 pp. eadd1268-eadd1268 [ DOI: doi:10.1126/science.add1268 Pubmed: 36227998 ]
- Transient receptor potential cation channel subfamily m member 8 (Complex from Ficedula albicollis)
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
- Transient receptor potential cation channel subfamily m member 8 (131 kDa, Protein from Ficedula albicollis)
Chitin Synthase 2 from Candida albicans bound to Nikkomycin Z
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 7stn
Q-score: 0.498
Ren Z, Chhetri A, Guan Z, Suo Y, Yokoyama K, Lee SY
Nat Struct Mol Biol (2022) 29 pp. 653-664 [ DOI: doi:10.1038/s41594-022-00791-x Pubmed: 35788183 ]
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Chitin synthase 2 from candida albicans bound to nikkomycin z (Complex from Candida albicans)
- Chitin synthase (119 kDa, Protein from Candida albicans)
- (2s)-{[(2s,3s,4s)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}[(2r,3s,4r,5r)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid (non-preferred name) (495 Da, Ligand)
Chitin Synthase 2 from Candida albicans bound to polyoxin D
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 7sto
Q-score: 0.534
Ren Z, Chhetri A, Guan Z, Suo Y, Yokoyama K, Lee SY
Nat Struct Mol Biol (2022) 29 pp. 653-664 [ DOI: doi:10.1038/s41594-022-00791-x Pubmed: 35788183 ]
- 1-{(2r,3r,4s,5r)-5-[(s)-{[(2s,3s,4s)-2-amino-5-(carbamoyloxy)-3,4-dihydroxypentanoyl]amino}(carboxy)methyl]-3,4-dihydroxyoxolan-2-yl}-2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid (non-preferred name) (521 Da, Ligand)
- Chitin synthase 2 from candida albicans bound to polyoxin d (Complex from Candida albicans)
- Chitin synthase (119 kDa, Protein from Candida albicans)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)