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)
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 [ Pubmed: 38956111 DOI: doi:10.1038/s41467-024-49899-2 ]
- Solute carrier family 23 member 1 (64 kDa, Protein from Homo sapiens)
- Human svct1 dimer in an apo inward-open state (Complex from Homo sapiens)
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Palmitic acid (256 Da, Ligand)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Cholesterol (386 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 [ Pubmed: 38956111 DOI: doi:10.1038/s41467-024-49899-2 ]
- Solute carrier family 23 member 1 (64 kDa, Protein from Homo sapiens)
- Ascorbic acid (176 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Palmitic acid (256 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Human svct1 dimer in a substrate-bound inward-open state (Complex from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Water (18 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 [ Pubmed: 38956111 DOI: doi:10.1038/s41467-024-49899-2 ]
- Solute carrier family 23 member 1 (64 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Palmitic acid (256 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Human svct1 dimer in an apo occluded state (Complex from Homo sapiens)
- Water (18 Da, Ligand)
Cryo-EM structure of the TnpB-omegaRNA-target DNA ternary complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8h1j
Q-score: 0.453
Nakagawa R, Hirano H, Omura SN, Nety S, Kannan S, Altae-Tran H, Yao X, Sakaguchi Y, Ohira T, Wu WY, Nakayama H, Shuto Y, Tanaka T, Sano FK, Kusakizako T, Kise Y, Itoh Y, Dohmae N, van der Oost J, Suzuki T, Zhang F, Nureki O
Nature (2023) 616 pp. 390-397 [ DOI: doi:10.1038/s41586-023-05933-9 Pubmed: 37020030 ]
- Rna-guided dna endonuclease tnpb (46 kDa, Protein from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
- Zinc ion (65 Da, Ligand)
- Non-target strand (10 kDa, DNA from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
- Tnpb-omegarna-target dna ternary complex (Complex from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
- Omegarna (130-mer) (79 kDa, RNA from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
- Target strand (10 kDa, DNA from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
Cryo-EM structure of the Cas12m2-crRNA-target DNA full R-loop complex
Resolution: 2.87 Å
EM Method: Single-particle
Fitted PDBs: 8hhl
Q-score: 0.547
Omura SN, Nakagawa R, Sudfeld C, Villegas Warren R, Wu WY, Hirano H, Laffeber C, Kusakizako T, Kise Y, Lebbink JHG, Itoh Y, van der Oost J, Nureki O
Nat Struct Mol Biol (2023) 30 pp. 1172-1182 [ DOI: doi:10.1038/s41594-023-01042-3 Pubmed: 37460897 ]
- Crrna-target dna (Complex)
- Zinc ion (65 Da, Ligand)
- Ts (36-mer) (10 kDa, DNA from Mycolicibacterium mucogenicum)
- Crrna (Complex)
- Cas12m2 (Complex)
- Cas12m2-crrna-target dna (Complex from Mycolicibacterium mucogenicum)
- Crrna (56-mer) (18 kDa, RNA from Mycolicibacterium mucogenicum)
- Nts (36-mer) (11 kDa, DNA from Mycolicibacterium mucogenicum)
- Target dna (Complex)
- Magnesium ion (24 Da, Ligand)
- Cas12m2 (66 kDa, Protein from Mycolicibacterium mucogenicum)
Cryo-EM structure of the Cas12m2-crRNA-target DNA ternary complex intermediate state
Resolution: 3.08 Å
EM Method: Single-particle
Fitted PDBs: 8hhm
Q-score: 0.454
Omura SN, Nakagawa R, Sudfeld C, Villegas Warren R, Wu WY, Hirano H, Laffeber C, Kusakizako T, Kise Y, Lebbink JHG, Itoh Y, van der Oost J, Nureki O
Nat Struct Mol Biol (2023) 30 pp. 1172-1182 [ DOI: doi:10.1038/s41594-023-01042-3 Pubmed: 37460897 ]
- Crrna-target dna (Complex)
- Zinc ion (65 Da, Ligand)
- Crrna (Complex)
- Cas12m2 (Complex)
- Dna (36-mer) (10 kDa, DNA from Mycolicibacterium mucogenicum)
- Cas12m2-crrna-target dna (Complex from Mycolicibacterium mucogenicum)
- Dna (36-mer) (11 kDa, DNA from Mycolicibacterium mucogenicum)
- Target dna (Complex)
- Magnesium ion (24 Da, Ligand)
- Rna (56-mer) (18 kDa, RNA from Mycolicibacterium mucogenicum)
- Cas12m2 (66 kDa, Protein from Mycolicibacterium mucogenicum)
Cryo-EM structure of the Cas12m2-crRNA binary complex
Resolution: 3.73 Å
EM Method: Single-particle
Fitted PDBs: 8hio
Q-score: 0.331
Omura SN, Nakagawa R, Sudfeld C, Villegas Warren R, Wu WY, Hirano H, Laffeber C, Kusakizako T, Kise Y, Lebbink JHG, Itoh Y, van der Oost J, Nureki O
Nat Struct Mol Biol (2023) 30 pp. 1172-1182 [ DOI: doi:10.1038/s41594-023-01042-3 Pubmed: 37460897 ]
- Cas12m2-crrna (Complex from Mycolicibacterium mucogenicum)
- Zinc ion (65 Da, Ligand)
- Cas12m2 (66 kDa, Protein from Mycolicibacterium mucogenicum)
- Crrna (Complex)
- Cas12m2 (Complex)
- Rna (56-mer) (18 kDa, RNA from Mycolicibacterium mucogenicum)
- Magnesium ion (24 Da, Ligand)