Resolution: 4.9 Å
EM Method: Single-particle
Fitted PDBs: 8ydx
Q-score: 0.237
Nakamura S, Tanimura Y, Nomura R, Suzuki H, Nishikawa K, Kamegawa A, Numoto N, Tanaka A, Kawabata S, Sakaguchi S, Emi A, Suzuki Y, Fujiyoshi Y
To Be Published
- Sars-cov-2 spike ectodomain (hexapro, omicron ba.2 variant) in complex with cespiace (Complex from Severe acute respiratory syndrome coronavirus 2)
- Cespiace (4 kDa, Protein from synthetic construct)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Resolution: 8.0 Å
EM Method: Single-particle
Fitted PDBs: 8ydy
Q-score: 0.084
Nakamura S, Tanimura Y, Nomura R, Suzuki H, Nishikawa K, Kamegawa A, Numoto N, Tanaka A, Kawabata S, Sakaguchi S, Emi A, Suzuki Y, Fujiyoshi Y
To Be Published
- Cespiace (4 kDa, Protein from synthetic construct)
- Sars-cov-2 spike ectodomain (hexapro, omicron ba.5 variant) in complex with cespiace (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Resolution: 5.2 Å
EM Method: Single-particle
Fitted PDBs: 8ydz
Q-score: 0.2
Nakamura S, Tanimura Y, Nomura R, Suzuki H, Nishikawa K, Kamegawa A, Numoto N, Tanaka A, Kawabata S, Sakaguchi S, Emi A, Suzuki Y, Fujiyoshi Y
To Be Published
- Cespiace (4 kDa, Protein from synthetic construct)
- Sars-cov-2 spike ectodomain (hexapro, omicron ba.5 variant) in complex with cespiace (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Structure of arginine oxidase from Pseudomonas sp. TRU 7192
Resolution: 2.34 Å
EM Method: Single-particle
Fitted PDBs: 8jt7
Q-score: 0.689
Yamaguchi H, Takahashi K, Numoto N, Suzuki H, Tatsumi M, Kamegawa A, Nishikawa K, Asano Y, Mizukoshi T, Miyano H, Fujiyoshi Y, Sugiki M
J.Biochem. (2025) 177 pp. 27-36 [ Pubmed: 39420599 DOI: doi:10.1093/jb/mvae070 ]
- Water (18 Da, Ligand)
- Homooctamer of arginine oxidase (540 kDa, Complex from Pseudomonas sp.)
- Amine oxidoreductase (67 kDa, Protein from Pseudomonas sp.)
- Flavin-adenine dinucleotide (785 Da, Ligand)
Cryo-EM structure of the J-K-St region of EMCV IRES in complex with eIF4G-HEAT1 and eIF4A
Resolution: 3.76 Å
EM Method: Single-particle
Fitted PDBs: 8huj
Q-score: 0.406
Imai S, Suzuki H, Fujiyoshi Y, Shimada I
Nat Commun (2023) 14 pp. 4977-4977 [ DOI: doi:10.1038/s41467-023-40582-6 Pubmed: 37640715 ]
- Ires rna (j-k-st) (34 kDa, RNA from Encephalomyocarditis virus)
- Water (18 Da, Ligand)
- Ternary complex of the j-k-st region of emcv ires with eif4a and eif4g-heat1 (Complex from Homo sapiens)
- Eukaryotic initiation factor 4a-i (48 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Eukaryotic translation initiation factor 4 gamma 1 (31 kDa, Protein from Homo sapiens)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8j7r
Q-score: 0.407
Imai S, Suzuki H, Fujiyoshi Y, Shimada I
Nat Commun (2023) 14 pp. 4977-4977 [ DOI: doi:10.1038/s41467-023-40582-6 Pubmed: 37640715 ]
- Ires rna (j-k-st) (34 kDa, RNA from Encephalomyocarditis virus)
- Ternary complex of the j-k-st region of emcv ires with eif4a and eif4g-heat1 (Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Eukaryotic translation initiation factor 4 gamma 1 (31 kDa, Protein from Homo sapiens)
Cryo-EM structure of the N-terminal deletion mutant of human pannexin-1 in a nanodisc
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7wsv
Q-score: 0.325
Kuzuya M, Hirano H, Hayashida K, Watanabe M, Kobayashi K, Terada T, Mahmood MI, Tama F, Tani K, Fujiyoshi Y, Oshima A
Sci Signal (2022) 15 pp. eabg6941-eabg6941 [ DOI: doi:10.1126/scisignal.abg6941 Pubmed: 35133866 ]
Cryo-EM structure of human pannexin-1 in a nanodisc
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7f8j
Q-score: 0.48
Kuzuya M, Hirano H, Hayashida K, Watanabe M, Kobayashi K, Terada T, Mahmood MI, Tama F, Tani K, Fujiyoshi Y, Oshima A
Sci Signal (2022) 15 pp. eabg6941-eabg6941 [ DOI: doi:10.1126/scisignal.abg6941 Pubmed: 35133866 ]
- Heptamar of human pannexin-1 channel in a nanodisc (Complex from Homo sapiens)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Pannexin-1 (48 kDa, Protein from Homo sapiens)
Human pannexin-1 showing a conformational change in the N-terminal domain and blocked pore
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7f8n
Q-score: 0.488
Kuzuya M, Hirano H, Hayashida K, Watanabe M, Kobayashi K, Terada T, Mahmood MI, Tama F, Tani K, Fujiyoshi Y, Oshima A
Sci Signal (2022) 15 pp. eabg6941-eabg6941 [ DOI: doi:10.1126/scisignal.abg6941 Pubmed: 35133866 ]
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Pannexin-1 (48 kDa, Protein from Homo sapiens)
- Human pannexin-1 (Complex from Homo sapiens)
Cryo-EM structure of the C-terminal deletion mutant of human PANX1 in a nanodisc
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7f8o
Q-score: 0.444
Kuzuya M, Hirano H, Hayashida K, Watanabe M, Kobayashi K, Terada T, Mahmood MI, Tama F, Tani K, Fujiyoshi Y, Oshima A
Sci Signal (2022) 15 pp. eabg6941-eabg6941 [ DOI: doi:10.1126/scisignal.abg6941 Pubmed: 35133866 ]
- Heptamar of human pannexin-1 channel in a nanodisc (Complex from Homo sapiens)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Pannexin-1 (48 kDa, Protein from Homo sapiens)