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
- Water (18 Da, Ligand)
- Gprotein gamma-2 (Complex from Bos taurus)
- Pth-pth1r-gq complex (Complex)
- Parathyroid hormone/parathyroid hormone-related peptide receptor (63 kDa, Protein from Homo sapiens)
- Gprotein beta-1 (Complex from Rattus rattus)
- Parathyroid hormone 1 receptor (Complex from Homo sapiens)
- Mini-g (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(q) subunit alpha-1 (minigq) (27 kDa, Protein from Homo sapiens)
- Scfv16 (Complex from Mus musculus)
- Scfv16 (27 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Rattus rattus)
- Parathyroid hormone (4 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Parathyroid hormone (Complex from Homo sapiens)
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
- Water (18 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Pth-pth1r-gq complex (Complex)
- Parathyroid hormone/parathyroid hormone-related peptide receptor (63 kDa, Protein from Homo sapiens)
- Minigq (Complex from Homo sapiens)
- Pth1r (Complex from Homo sapiens)
- Scfv16 (Complex from Mus musculus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit gamma-2 (Complex from Bos taurus)
- Scfv16 (27 kDa, Protein from Mus musculus)
- Pth (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Rattus rattus)
- Parathyroid hormone (4 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (minigq) (27 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (Complex from Rattus rattus)
Human sodium-dependent vitamin C transporter 1 in an apo inward-open state
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8jez
Q-score: 0.616
Kobayashi TA, Shimada H, Sano FK, Itoh Y, Enoki S, Okada Y, Kusakizako T, Nureki O
Nat Commun (2024) 15 pp. 5569-5569 [ DOI: doi:10.1038/s41467-024-49899-2 Pubmed: 38956111 ]
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Solute carrier family 23 member 1 (64 kDa, Protein from Homo sapiens)
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Human svct1 dimer in an apo inward-open state (Complex from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
Human sodium-dependent vitamin C transporter 1 bound to L-ascorbic acid in an inward-open state
Kobayashi TA, Shimada H, Sano FK, Itoh Y, Enoki S, Okada Y, Kusakizako T, Nureki O
Nat Commun (2024) 15 pp. 5569-5569 [ DOI: doi:10.1038/s41467-024-49899-2 Pubmed: 38956111 ]
- Water (18 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Solute carrier family 23 member 1 (64 kDa, Protein from Homo sapiens)
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Cholesterol (386 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Human svct1 dimer in a substrate-bound inward-open state (Complex from Homo sapiens)
- Ascorbic acid (176 Da, Ligand)
Human sodium-dependent vitamin C transporter 1 in an apo occluded state
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8jf1
Q-score: 0.595
Kobayashi TA, Shimada H, Sano FK, Itoh Y, Enoki S, Okada Y, Kusakizako T, Nureki O
Nat Commun (2024) 15 pp. 5569-5569 [ DOI: doi:10.1038/s41467-024-49899-2 Pubmed: 38956111 ]
- Cholesterol (386 Da, Ligand)
- Water (18 Da, Ligand)
- Human svct1 dimer in an apo occluded state (Complex from Homo sapiens)
- Solute carrier family 23 member 1 (64 kDa, Protein from Homo sapiens)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
Small subunit of yeast mitochondrial ribosome in complex with METTL17/Rsm22.
Resolution: 2.57 Å
EM Method: Single-particle
Fitted PDBs: 8om2
Q-score: 0.602
Ast T, Itoh Y, Sadre S, McCoy JG, Namkoong G, Wengrod JC, Chicherin I, Joshi PR, Kamenski P, Suess DLM, Amunts A, Mootha VK
Mol Cell (2024) 84 pp. 359- [ DOI: doi:10.1016/j.molcel.2023.12.016 Pubmed: 38199006 ]
- 37s ribosomal protein s5, mitochondrial (34 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s9, mitochondrial (31 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp21, mitochondrial (20 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp2, mitochondrial (13 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s25, mitochondrial (30 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s7, mitochondrial (27 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp17, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein sws2, mitochondrial (16 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 37s ribosomal protein s10, mitochondrial (23 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s23, mitochondrial (50 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s19, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein pet123, mitochondrial (36 kDa, Protein from Saccharomyces cerevisiae)
- Protein fyv4, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- 15s mitochondrial rrna (528 kDa, RNA from Saccharomyces cerevisiae)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Mitochondrial mrna-processing protein cox24 (12 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s24, mitochondrial (37 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp10, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- Potassium ion (39 Da, Ligand)
- 37s ribosomal protein s28, mitochondrial (33 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein nam9, mitochondrial (56 kDa, Protein from Saccharomyces cerevisiae)
- Small subunit of mitochondrial ribosome in complex with mettl17/rsm22 (Complex from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp51, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s12, mitochondrial (16 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s26, mitochondrial (30 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- 37s ribosomal protein s8, mitochondrial (17 kDa, Protein from Saccharomyces cerevisiae)
- Probable s-adenosyl-l-methionine-dependent rna methyltransferase rsm22, mitochondrial (72 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s35, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s18, mitochondrial (24 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s17, mitochondrial (27 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp13, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp4, mitochondrial (44 kDa, Protein from Saccharomyces cerevisiae)
- Mitochondrial 37s ribosomal protein s27 (12 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein rsm18, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp1, mitochondrial (36 kDa, Protein from Saccharomyces cerevisiae)
- 3-hydroxyisobutyryl-coa hydrolase, mitochondrial (56 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s16, mitochondrial (13 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Ribosomal protein var1, mitochondrial (47 kDa, Protein from Saccharomyces cerevisiae)
Small subunit of yeast mitochondrial ribosome in complex with IF3/Aim23.
Resolution: 2.87 Å
EM Method: Single-particle
Fitted PDBs: 8om3
Q-score: 0.564
Ast T, Itoh Y, Sadre S, McCoy JG, Namkoong G, Wengrod JC, Chicherin I, Joshi PR, Kamenski P, Suess DLM, Amunts A, Mootha VK
Mol Cell (2024) 84 pp. 359- [ DOI: doi:10.1016/j.molcel.2023.12.016 Pubmed: 38199006 ]
- 37s ribosomal protein s5, mitochondrial (34 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s9, mitochondrial (31 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp21, mitochondrial (20 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp2, mitochondrial (13 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s25, mitochondrial (30 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s7, mitochondrial (27 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp17, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein sws2, mitochondrial (16 kDa, Protein from Saccharomyces cerevisiae)
- Altered inheritance of mitochondria protein 23, mitochondrial (42 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 37s ribosomal protein s10, mitochondrial (23 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s23, mitochondrial (50 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s19, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein pet123, mitochondrial (36 kDa, Protein from Saccharomyces cerevisiae)
- Protein fyv4, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- 15s mitochondrial rrna (528 kDa, RNA from Saccharomyces cerevisiae)
- 37s ribosomal protein s8, mitochondrial (17 kDa, Protein from Saccharomyces cerevisiae)
- Mitochondrial mrna-processing protein cox24 (12 kDa, Protein from Saccharomyces cerevisiae)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 37s ribosomal protein s24, mitochondrial (37 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp10, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- Potassium ion (39 Da, Ligand)
- 37s ribosomal protein s28, mitochondrial (33 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein nam9, mitochondrial (56 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp51, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s12, mitochondrial (16 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s26, mitochondrial (30 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- Small subunit of mitochondrial ribosome in complex with if3/aim23 (Complex from Saccharomyces cerevisiae)
- 37s ribosomal protein s35, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s18, mitochondrial (24 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s17, mitochondrial (27 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp13, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp4, mitochondrial (44 kDa, Protein from Saccharomyces cerevisiae)
- Mitochondrial 37s ribosomal protein s27 (12 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein rsm18, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp1, mitochondrial (36 kDa, Protein from Saccharomyces cerevisiae)
- 3-hydroxyisobutyryl-coa hydrolase, mitochondrial (56 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s16, mitochondrial (13 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Ribosomal protein var1, mitochondrial (47 kDa, Protein from Saccharomyces cerevisiae)
Small subunit of yeast mitochondrial ribosome.
Resolution: 2.32 Å
EM Method: Single-particle
Fitted PDBs: 8om4
Q-score: 0.654
Ast T, Itoh Y, Sadre S, McCoy JG, Namkoong G, Wengrod JC, Chicherin I, Joshi PR, Kamenski P, Suess DLM, Amunts A, Mootha VK
Mol Cell (2024) 84 pp. 359- [ Pubmed: 38199006 DOI: doi:10.1016/j.molcel.2023.12.016 ]
- Small subunit of mitochondrial ribosome (Complex from Saccharomyces cerevisiae)
- 37s ribosomal protein pet123, mitochondrial (36 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s23, mitochondrial (50 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s35, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- Ribosomal protein var1, mitochondrial (47 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s25, mitochondrial (30 kDa, Protein from Saccharomyces cerevisiae)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 37s ribosomal protein mrp21, mitochondrial (20 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp1, mitochondrial (36 kDa, Protein from Saccharomyces cerevisiae)
- Mitochondrial 37s ribosomal protein s27 (12 kDa, Protein from Saccharomyces cerevisiae)
- 3-hydroxyisobutyryl-coa hydrolase, mitochondrial (56 kDa, Protein from Saccharomyces cerevisiae)
- Potassium ion (39 Da, Ligand)
- 37s ribosomal protein s8, mitochondrial (17 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s16, mitochondrial (13 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s5, mitochondrial (34 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein rsm18, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s26, mitochondrial (30 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp10, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein sws2, mitochondrial (16 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s19, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein nam9, mitochondrial (56 kDa, Protein from Saccharomyces cerevisiae)
- Protein fyv4, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- 37s ribosomal protein mrp4, mitochondrial (44 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s18, mitochondrial (24 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s17, mitochondrial (27 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s28, mitochondrial (33 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp51, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp13, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s12, mitochondrial (16 kDa, Protein from Saccharomyces cerevisiae)
- Mitochondrial mrna-processing protein cox24 (12 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s10, mitochondrial (23 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp17, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp2, mitochondrial (13 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s9, mitochondrial (31 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 15s mitochondrial rrna (528 kDa, RNA from Saccharomyces cerevisiae)
- 37s ribosomal protein s7, mitochondrial (27 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s24, mitochondrial (37 kDa, Protein from Saccharomyces cerevisiae)
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 [ Pubmed: 37647387 DOI: doi:10.1126/scitranslmed.adi2623 ]
- Ace2 (Complex from Homo sapiens)
- Angiotensin-converting enzyme 2 (73 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Spike glycoprotein (138 kDa, Protein from synthetic construct)
- 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)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM structure of the AsCas12f-sgRNA-target DNA ternary complex
Resolution: 3.08 Å
EM Method: Single-particle
Fitted PDBs: 8j12
Q-score: 0.479
Hino T, Omura SN, Nakagawa R, Togashi T, Takeda SN, Hiramoto T, Tasaka S, Hirano H, Tokuyama T, Uosaki H, Ishiguro S, Kagieva M, Yamano H, Ozaki Y, Motooka D, Mori H, Kirita Y, Kise Y, Itoh Y, Matoba S, Aburatani H, Yachie N, Karvelis T, Siksnys V, Ohmori T, Hoshino A, Nureki O
Cell (2023) 186 pp. 4920-4935.e23 [ DOI: doi:10.1016/j.cell.2023.08.031 Pubmed: 37776859 ]
- Rna (247-mer) (72 kDa, RNA from Acidibacillus sulfooxidans)
- Ascas12f-sgrna-target dna (Complex from Mycolicibacterium mucogenicum)
- Transposase is605 orfb c-terminal domain-containing protein (49 kDa, Protein from Acidibacillus sulfuroxidans)
- Dna (38-mer) (11 kDa, DNA from Acidibacillus sulfooxidans)
- Magnesium ion (24 Da, Ligand)
- Dna (38-mer) (11 kDa, DNA from Acidibacillus sulfooxidans)
- Zinc ion (65 Da, Ligand)