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, sulfate or salicylate
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 [ Pubmed: 36266333 DOI: 10.1038/s41467-022-34017-x ]
Image sets:
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)