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 ]
- 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-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)
- Phospho-n-acetylmuramoyl-pentapeptide-transferase (40 kDa, Protein 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 ]
- (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)
- Complex of mray aa dimer with nanobody bound (200 kDa, Complex from Aquifex aeolicus VF5)
- Phospho-n-acetylmuramoyl-pentapeptide-transferase (40 kDa, Protein from Aquifex aeolicus VF5)
- Water (18 Da, Ligand)
- Mrayaa nanobody (15 kDa, Protein from Lama glama)
Thermostabilized human prestin in complex with chloride
Resolution: 3.52 Å
EM Method: Single-particle
Fitted PDBs: 7v73
Q-score: 0.488
Futamata H, Fukuda M, Umeda R, Yamashita K, Tomita A, Takahashi S, Shikakura T, Hayashi S, Kusakizako T, Nishizawa T, Homma K, Nureki O
Nat Commun (2022) 13 pp. 6208-6208 [ Pubmed: 36266333 DOI: doi:10.1038/s41467-022-34017-x ]
- Prestin (82 kDa, Protein from Homo sapiens)
- Prestin in complex with chloride ion (Complex from Homo sapiens)
- Chloride ion (35 Da, Ligand)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Cholesterol (386 Da, Ligand)
Thermostabilized human prestin in complex with sulfate
Resolution: 3.63 Å
EM Method: Single-particle
Fitted PDBs: 7v74
Q-score: 0.5
Futamata H, Fukuda M, Umeda R, Yamashita K, Tomita A, Takahashi S, Shikakura T, Hayashi S, Kusakizako T, Nishizawa T, Homma K, Nureki O
Nat Commun (2022) 13 pp. 6208-6208 [ Pubmed: 36266333 DOI: doi:10.1038/s41467-022-34017-x ]
- Prestin (82 kDa, Protein from Homo sapiens)
- Prestin in complex with chloride ion (Complex from Homo sapiens)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Sulfate ion (96 Da, Ligand)
- Cholesterol (386 Da, Ligand)
Thermostabilized human prestin in complex with salicylate
Resolution: 3.57 Å
EM Method: Single-particle
Fitted PDBs: 7v75
Q-score: 0.488
Futamata H, Fukuda M, Umeda R, Yamashita K, Tomita A, Takahashi S, Shikakura T, Hayashi S, Kusakizako T, Nishizawa T, Homma K, Nureki O
Nat Commun (2022) 13 pp. 6208-6208 [ Pubmed: 36266333 DOI: doi:10.1038/s41467-022-34017-x ]
- 2-hydroxybenzoic acid (138 Da, Ligand)
- Prestin (82 kDa, Protein from Homo sapiens)
- Prestin in complex with chloride ion (Complex from Homo sapiens)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Cholesterol (386 Da, Ligand)
cryo-EM structure of human ATG9A in amphipols
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7jlo
Q-score: 0.536
Maeda S, Yamamoto H, Kinch LN, Garza CM, Takahashi S, Otomo C, Grishin NV, Forli S, Mizushima N, Otomo T
Nat Struct Mol Biol (2020) 27 pp. 1194-1201 [ DOI: doi:10.1038/s41594-020-00520-2 Pubmed: 33106659 ]
- Human atg9a in amphipols a8-35 (Cellular component from Homo sapiens)
- Autophagy-related protein 9a (66 kDa, Protein from Homo sapiens)
cryo-EM structure of human ATG9A in nanodiscs
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7jlp
Q-score: 0.552
Maeda S, Yamamoto H, Kinch LN, Garza CM, Takahashi S, Otomo C, Grishin NV, Forli S, Mizushima N, Otomo T
Nat Struct Mol Biol (2020) 27 pp. 1194-1201 [ DOI: doi:10.1038/s41594-020-00520-2 Pubmed: 33106659 ]
cryo-EM structure of human ATG9A in LMNG micelles
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7jlq
Q-score: 0.297
Maeda S, Yamamoto H, Kinch LN, Garza CM, Takahashi S, Otomo C, Grishin NV, Forli S, Mizushima N, Otomo T
Nat Struct Mol Biol (2020) 27 pp. 1194-1201 [ DOI: doi:10.1038/s41594-020-00520-2 Pubmed: 33106659 ]
- Human atg9a in lmng micelles (Cellular component from Homo sapiens)
- Autophagy-related protein 9a (66 kDa, Protein from Homo sapiens)