Cryo-EM structure of PTH-PTH1R-Gq (upright state)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9jr2
Q-score: 0.492
Sano FK, Kobayashi K, Kawakami K, Akasaka H, Kobayashi TA, Tanaka T, Okamoto HH, Hirano H, Kusakizako T, Shihoya W, Kise Y, Itoh Y, Ishitani R, Okada Y, Inoue A, Nureki O
To Be Published
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Gprotein gamma-2 (Complex from Bos taurus)
- Mini-g (Complex from Homo sapiens)
- Parathyroid hormone (4 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Rattus rattus)
- Scfv16 (27 kDa, Protein from Mus musculus)
- Parathyroid hormone/parathyroid hormone-related peptide receptor (63 kDa, Protein from Homo sapiens)
- Parathyroid hormone 1 receptor (Complex from Homo sapiens)
- Gprotein beta-1 (Complex from Rattus rattus)
- Parathyroid hormone (Complex from Homo sapiens)
- Scfv16 (Complex from Mus musculus)
- Water (18 Da, Ligand)
- Guanine nucleotide-binding protein g(q) subunit alpha-1 (minigq) (27 kDa, Protein from Homo sapiens)
- Pth-pth1r-gq complex (Complex)
Cryo-EM structure of PTH-PTH1R-Gq (tilted state)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9jr3
Q-score: 0.487
Sano FK, Kobayashi K, Kawakami K, Akasaka H, Kobayashi TA, Tanaka T, Okamoto HH, Hirano H, Kusakizako T, Shihoya W, Kise Y, Itoh Y, Ishitani R, Okada Y, Inoue A, Nureki O
To Be Published
- Pth (Complex from Homo sapiens)
- Minigq (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit gamma-2 (Complex from Bos taurus)
- Pth1r (Complex from Homo sapiens)
- Parathyroid hormone (4 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Rattus rattus)
- Scfv16 (27 kDa, Protein from Mus musculus)
- Parathyroid hormone/parathyroid hormone-related peptide receptor (63 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (minigq) (27 kDa, Protein from Homo sapiens)
- Scfv16 (Complex from Mus musculus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (Complex from Rattus rattus)
- Water (18 Da, Ligand)
- Pth-pth1r-gq complex (Complex)
RBD of SARS-CoV2 spike protein with ACE2 decoy
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8jje
Q-score: 0.488
Urano E, Itoh Y, Suzuki T, Sasaki T, Kishikawa JI, Akamatsu K, Higuchi Y, Sakai Y, Okamura T, Mitoma S, Sugihara F, Takada A, Kimura M, Nakao S, Hirose M, Sasaki T, Koketsu R, Tsuji S, Yanagida S, Shioda T, Hara E, Matoba S, Matsuura Y, Kanda Y, Arase H, Okada M, Takagi J, Kato T, Hoshino A, Yasutomi Y, Saito A, Okamoto T
Sci Transl Med (2023) 15 pp. eadi2623-eadi2623 [ DOI: doi:10.1126/scitranslmed.adi2623 Pubmed: 37647387 ]
- Zinc ion (65 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Rbd of sars-cov2 spike protein with ace2 decoy. (460 kDa, Complex)
- Sulfate ion (96 Da, Ligand)
- Sars-cov2 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Ace2 (Complex from Homo sapiens)
- Angiotensin-converting enzyme 2 (73 kDa, Protein from Homo sapiens)
- Spike glycoprotein (138 kDa, Protein from synthetic construct)
- Water (18 Da, Ligand)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7x8w
Q-score: 0.53
Takeshita M, Fukuyama H, Kamada K, Matsumoto T, Makino-Okamura C, Uchikubo-Kamo T, Tomabechi Y, Hanada K, Moriyama S, Takahashi Y, Ishigaki H, Nakayama M, Nguyen CT, Kitagawa Y, Itoh Y, Imai M, Maemura T, Furusawa Y, Ueki H, Iwatsuki-Horimoto K, Ito M, Yamayoshi S, Kawaoka Y, Shirouzu M, Ishii M, Saya H, Kondo Y, Kaneko Y, Suzuki K, Fukunaga K, Takeuchi T
iScience (2022) 25 pp. 105596-105596 [ DOI: doi:10.1016/j.isci.2022.105596 Pubmed: 36406861 ]
- The sars-cov-2 spike protein bound with the fab fragment of a human neutralizing antibody ab354 (560 kDa, Complex from Homo sapiens)
- Ab354 light chain (25 kDa, Protein from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ab354 heavy chain (28 kDa, Protein from Homo sapiens)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7x8y
Q-score: 0.318
Takeshita M, Fukuyama H, Kamada K, Matsumoto T, Makino-Okamura C, Uchikubo-Kamo T, Tomabechi Y, Hanada K, Moriyama S, Takahashi Y, Ishigaki H, Nakayama M, Nguyen CT, Kitagawa Y, Itoh Y, Imai M, Maemura T, Furusawa Y, Ueki H, Iwatsuki-Horimoto K, Ito M, Yamayoshi S, Kawaoka Y, Shirouzu M, Ishii M, Saya H, Kondo Y, Kaneko Y, Suzuki K, Fukunaga K, Takeuchi T
iScience (2022) 25 pp. 105596-105596 [ DOI: doi:10.1016/j.isci.2022.105596 Pubmed: 36406861 ]
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- The sars-cov-2 spike protein bound with the fab fragment of a human neutralizing antibody ab159 (560 kDa, Complex from Homo sapiens)
- Ab159 light chain (26 kDa, Protein from Homo sapiens)
- Ab159 heavy chain (28 kDa, Protein from Homo sapiens)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7x8z
Q-score: 0.368
Takeshita M, Fukuyama H, Kamada K, Matsumoto T, Makino-Okamura C, Uchikubo-Kamo T, Tomabechi Y, Hanada K, Moriyama S, Takahashi Y, Ishigaki H, Nakayama M, Nguyen CT, Kitagawa Y, Itoh Y, Imai M, Maemura T, Furusawa Y, Ueki H, Iwatsuki-Horimoto K, Ito M, Yamayoshi S, Kawaoka Y, Shirouzu M, Ishii M, Saya H, Kondo Y, Kaneko Y, Suzuki K, Fukunaga K, Takeuchi T
iScience (2022) 25 pp. 105596-105596 [ DOI: doi:10.1016/j.isci.2022.105596 Pubmed: 36406861 ]
- The sars-cov-2 spike protein bound with the fab fragment of a human neutralizing antibody ab354 (560 kDa, Complex from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ab188 light chain (27 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ab188 heavy chain (28 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7x90
Q-score: 0.392
Takeshita M, Fukuyama H, Kamada K, Matsumoto T, Makino-Okamura C, Uchikubo-Kamo T, Tomabechi Y, Hanada K, Moriyama S, Takahashi Y, Ishigaki H, Nakayama M, Nguyen CT, Kitagawa Y, Itoh Y, Imai M, Maemura T, Furusawa Y, Ueki H, Iwatsuki-Horimoto K, Ito M, Yamayoshi S, Kawaoka Y, Shirouzu M, Ishii M, Saya H, Kondo Y, Kaneko Y, Suzuki K, Fukunaga K, Takeuchi T
iScience (2022) 25 pp. 105596-105596 [ DOI: doi:10.1016/j.isci.2022.105596 Pubmed: 36406861 ]
- Ab326 heavy chain (28 kDa, Protein from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- The sars-cov-2 spike protein bound with the fab fragment of a human neutralizing antibody ab326 (560 kDa, Complex from Homo sapiens)
- Ab326 light chain (26 kDa, Protein from Homo sapiens)
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 7x91
Q-score: 0.321
Takeshita M, Fukuyama H, Kamada K, Matsumoto T, Makino-Okamura C, Uchikubo-Kamo T, Tomabechi Y, Hanada K, Moriyama S, Takahashi Y, Ishigaki H, Nakayama M, Nguyen CT, Kitagawa Y, Itoh Y, Imai M, Maemura T, Furusawa Y, Ueki H, Iwatsuki-Horimoto K, Ito M, Yamayoshi S, Kawaoka Y, Shirouzu M, Ishii M, Saya H, Kondo Y, Kaneko Y, Suzuki K, Fukunaga K, Takeuchi T
iScience (2022) 25 pp. 105596-105596 [ DOI: doi:10.1016/j.isci.2022.105596 Pubmed: 36406861 ]
- The sars-cov-2 spike protein bound with an fv-clasp form of a human neutralizing antibody ab496 (560 kDa, Complex from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- An fv-clasp version of the ab496 light chain (21 kDa, Protein from Homo sapiens)
- An fv-clasp version of the ab496 heavy chain (22 kDa, Protein from Homo sapiens)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7x92
Q-score: 0.348
Takeshita M, Fukuyama H, Kamada K, Matsumoto T, Makino-Okamura C, Uchikubo-Kamo T, Tomabechi Y, Hanada K, Moriyama S, Takahashi Y, Ishigaki H, Nakayama M, Nguyen CT, Kitagawa Y, Itoh Y, Imai M, Maemura T, Furusawa Y, Ueki H, Iwatsuki-Horimoto K, Ito M, Yamayoshi S, Kawaoka Y, Shirouzu M, Ishii M, Saya H, Kondo Y, Kaneko Y, Suzuki K, Fukunaga K, Takeuchi T
iScience (2022) 25 pp. 105596-105596 [ DOI: doi:10.1016/j.isci.2022.105596 Pubmed: 36406861 ]
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ab445 light chain (26 kDa, Protein from Homo sapiens)
- Ab445 heavy chain (28 kDa, Protein from Homo sapiens)
- The sars-cov-2 spike protein bound with the fab fragment of a human neutralizing antibody ab445 (560 kDa, Complex from Homo sapiens)
Structure of human mitochondrial 28S ribosome in complex with mitochondrial IF3
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 6rw4
Q-score: 0.599
Khawaja A, Itoh Y, Remes C, Spahr H, Yukhnovets O, Hofig H, Amunts A, Rorbach J
Nat Commun (2020) 11 pp. 2932-2932 [ DOI: doi:10.1038/s41467-020-16503-2 Pubmed: 32522994 ]
- 28s ribosomal protein s29, mitochondrial (45 kDa, Protein from Homo sapiens)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- 28s ribosomal protein s24, mitochondrial (19 kDa, Protein from Homo sapiens)
- 12s mitochondrial rrna (306 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s18c, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Spermine (202 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Homo sapiens)
- Ribosome (Complex from Homo sapiens)
- Water (18 Da, Ligand)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Homo sapiens)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from Homo sapiens)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Homo sapiens)
- Translation initiation factor if-3, mitochondrial (32 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s2, mitochondrial (33 kDa, Protein from Homo sapiens)
- Aurora kinase a-interacting protein (22 kDa, Protein from Homo sapiens)
- Streptomycin (581 Da, Ligand)
- If3 bound mitochondrial translation pre-initiation complex (1 MDa, Complex)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- If3 (Complex from Homo sapiens)
- 28s ribosomal protein s17, mitochondrial (14 kDa, Protein from Homo sapiens)
- Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 (13 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s25, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s26, mitochondrial (24 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s31, mitochondrial (45 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Homo sapiens)