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Cryo-EM structure of the panda P2X7 receptor in complex with PPADS
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8jv7
Q-score: 0.45
Sheng D, Yue CX, Jin F, Wang Y, Ichikawa M, Yu Y, Guo CR, Hattori M
eLife (2024) 12 [ Pubmed: 38578670 DOI: doi:10.7554/eLife.92829 ]
- 4-[(e)-[4-methanoyl-6-methyl-5-oxidanyl-3-(phosphonooxymethyl)pyridin-2-yl]diazenyl]benzene-1,3-disulfonic acid (511 Da, Ligand)
- P2x7 trimer (Complex from Ailuropoda melanoleuca)
- P2x purinoceptor (38 kDa, Protein from Ailuropoda melanoleuca)
- Water (18 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM structure of the panda P2X7 receptor in complex with PPNDS
Resolution: 3.34 Å
EM Method: Single-particle
Fitted PDBs: 8jv8
Q-score: 0.439
Sheng D, Yue CX, Jin F, Wang Y, Ichikawa M, Yu Y, Guo CR, Hattori M
eLife (2024) 12 [ Pubmed: 38578670 DOI: doi:10.7554/eLife.92829 ]
- 3-[(e)-{4-formyl-5-hydroxy-6-methyl-3-[(phosphonooxy)methyl]pyridin-2-yl}diazenyl]-7-nitronaphthalene-1,5-disulfonic acid (606 Da, Ligand)
- P2x7 trimer (Complex from Ailuropoda melanoleuca)
- P2x purinoceptor (38 kDa, Protein from Ailuropoda melanoleuca)
- Water (18 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM structure of the zebrafish P2X4 receptor in complex with BX430
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 8jv5
Q-score: 0.466
Shen C, Zhang Y, Cui W, Zhao Y, Sheng D, Teng X, Shao M, Ichikawa M, Wang J, Hattori M
Nat Commun (2023) 14 pp. 6437-6437 [ Pubmed: 37833294 DOI: doi:10.1038/s41467-023-42164-y ]
- 1-[2,6-bis(bromanyl)-4-propan-2-yl-phenyl]-3-pyridin-3-yl-urea (413 Da, Ligand)
- P2x4 trimer (120 kDa, Complex from Danio rerio)
- P2x purinoceptor (39 kDa, Protein from Danio rerio)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM structure of the zebrafish P2X4 receptor in complex with BAY-1797
Resolution: 3.43 Å
EM Method: Single-particle
Fitted PDBs: 8jv6
Q-score: 0.489
Shen C, Zhang Y, Cui W, Zhao Y, Sheng D, Teng X, Shao M, Ichikawa M, Wang J, Hattori M
Nat Commun (2023) 14 pp. 6437-6437 [ Pubmed: 37833294 DOI: doi:10.1038/s41467-023-42164-y ]
- P2x purinoceptor (39 kDa, Protein from Danio rerio)
- P2x4 trimer (120 kDa, Complex from Danio rerio)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- N-[4-(3-chloranylphenoxy)-3-sulfamoyl-phenyl]-2-phenyl-ethanamide (416 Da, Ligand)
The structure of the Tetrahymena thermophila outer dynein arm on doublet microtubule
Resolution: 8.0 Å
EM Method: Single-particle
Fitted PDBs: 7moq
Q-score: 0.067
Kubo S, Yang SK, Black CS, Dai D, Valente-Paterno M, Gaertig J, Ichikawa M, Bui KH
EMBO Rep (2021) 22 pp. e52911-e52911 [ Pubmed: 34338432 DOI: doi:10.15252/embr.202152911 ]
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila CU428)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Dynein light chain (12 kDa, Protein from Tetrahymena thermophila CU428)
- Tubulin beta chain (49 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein light chain (12 kDa, Protein from Tetrahymena thermophila CU428)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Outer dynein arm docking complex protein oda protein (63 kDa, Protein from Tetrahymena thermophila CU428)
- Tubulin alpha chain (49 kDa, Protein from Tetrahymena thermophila CU428)
- Outer arm dynein beta heavy chain (530 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein heavy chain, outer arm protein (534 kDa, Protein from Tetrahymena thermophila CU428)
- Thioredoxin (12 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein light chain roadblock-type 2 protein (14 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein light chain tctex-type 1 protein (13 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila CU428)
- Outer dynein arm docking complex protein oda protein (35 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein intermediate chain 2 (77 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein light chain (13 kDa, Protein from Tetrahymena thermophila CU428)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Dynein light chain roadblock-type 2 protein (18 kDa, Protein from Tetrahymena thermophila CU428)
- Flagellar outer dynein arm intermediate protein, putative (77 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein-1-alpha heavy chain, flagellar inner arm i1 complex protein, putative (475 kDa, Protein from Tetrahymena thermophila CU428)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Outer dynein arm complex from tetrahymena thermophila (2 MDa, Cellular component from Tetrahymena thermophila CU428)
- Docking complex 1/2 protein (11 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein light chain 2a (15 kDa, Protein from Tetrahymena thermophila CU428)
- Docking complex 1 protein (64 kDa, Protein from Tetrahymena thermophila CU428)
- Magnesium ion (24 Da, Ligand)
Cryo-EM structure of the 48-nm repeat unit of the doublet microtubule from Tetrahymena thermophila
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 6u0h
Q-score: 0.357
Ichikawa M, Khalifa AAZ, Kubo S, Dai D, Basu K, Maghrebi MAF, Vargas J, Bui KH
PNAS (2019) 116 pp. 19930-19938 [ DOI: doi:10.1073/pnas.1911119116 Pubmed: 31527277 ]
- Tubulin lattice (Complex from Tetrahymena thermophila)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Tubulin beta chain (49 kDa, Protein from Tetrahymena thermophila)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Tubulin alpha chain (49 kDa, Protein from Tetrahymena thermophila)
- 48nm-repeat of microtubule doublet (Cellular component from Tetrahymena thermophila)
Cryo-EM structure of 8nm repeat tubulin lattice of the ciliary microtubule doublet
Resolution: 5.7 Å
EM Method: Single-particle
Fitted PDBs: 5ubq
Q-score: 0.144
Ichikawa M, Liu D, Kastritis PL, Basu K, Hsu TC, Yang S, Bui KH
Nat Commun (2017) 8 pp. 15035-15035 [ DOI: doi:10.1038/ncomms15035 Pubmed: 28462916 ]
- 8nm-repeat tubulin lattice of microtubule doublet (Cellular component from Tetrahymena thermophila)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Tubulin beta chain (48 kDa, Protein from Tetrahymena thermophila)
- Tubulin alpha chain (48 kDa, Protein from Tetrahymena thermophila)
- Magnesium ion (24 Da, Ligand)
Cryo-EM map of protofilament of microtubule doublet
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 5ucy
Q-score: 0.264
Ichikawa M, Liu D, Kastritis PL, Basu K, Hsu TC, Yang S, Bui KH
Nat Commun (2017) 8 pp. 15035-15035 [ DOI: doi:10.1038/ncomms15035 Pubmed: 28462916 ]
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Tubulin beta chain (48 kDa, Protein from Tetrahymena thermophila)
- Protofilament from ciliary microtubule doublet (Cellular component from Tetrahymena thermophila)
- Tubulin alpha chain (48 kDa, Protein from Tetrahymena thermophila)
- Magnesium ion (24 Da, Ligand)