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)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- P2x purinoceptor (38 kDa, Protein from Ailuropoda melanoleuca)
- Water (18 Da, Ligand)
- P2x7 trimer (Complex from Ailuropoda melanoleuca)
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)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- P2x purinoceptor (38 kDa, Protein from Ailuropoda melanoleuca)
- Water (18 Da, Ligand)
- P2x7 trimer (Complex from Ailuropoda melanoleuca)
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 [ DOI: doi:10.1038/s41467-023-42164-y Pubmed: 37833294 ]
- 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)
- 1-[2,6-bis(bromanyl)-4-propan-2-yl-phenyl]-3-pyridin-3-yl-urea (413 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 [ DOI: doi:10.1038/s41467-023-42164-y Pubmed: 37833294 ]
- P2x4 trimer (120 kDa, Complex from Danio rerio)
- P2x purinoceptor (39 kDa, Protein from Danio rerio)
- N-[4-(3-chloranylphenoxy)-3-sulfamoyl-phenyl]-2-phenyl-ethanamide (416 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 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 [ DOI: doi:10.15252/embr.202152911 Pubmed: 34338432 ]
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein light chain 2a (15 kDa, Protein from Tetrahymena thermophila CU428)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Dynein light chain roadblock-type 2 protein (14 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein light chain (12 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila CU428)
- Docking complex 1/2 protein (11 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein intermediate chain 2 (77 kDa, Protein from Tetrahymena thermophila CU428)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dynein light chain (13 kDa, Protein from Tetrahymena thermophila CU428)
- Outer dynein arm complex from tetrahymena thermophila (2 MDa, Cellular component from Tetrahymena thermophila CU428)
- Dynein light chain roadblock-type 2 protein (18 kDa, Protein from Tetrahymena thermophila CU428)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Outer dynein arm docking complex protein oda protein (35 kDa, Protein from Tetrahymena thermophila CU428)
- Magnesium ion (24 Da, Ligand)
- Flagellar outer dynein arm intermediate protein, putative (77 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein light chain (10 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)
- Tubulin alpha chain (49 kDa, Protein from Tetrahymena thermophila CU428)
- Outer dynein arm docking complex protein oda protein (63 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein light chain tctex-type 1 protein (13 kDa, Protein from Tetrahymena thermophila CU428)
- Thioredoxin (12 kDa, Protein from Tetrahymena thermophila CU428)
- Tubulin beta chain (49 kDa, Protein from Tetrahymena thermophila CU428)
- Docking complex 1 protein (64 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein light chain (12 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein heavy chain, outer arm protein (534 kDa, Protein from Tetrahymena thermophila CU428)
- Outer arm dynein beta heavy chain (530 kDa, Protein from Tetrahymena thermophila CU428)
The inner junction complex of Chlamydomonas reinhardtii doublet microtubule
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6ve7
Q-score: 0.455
Khalifa AAZ, Ichikawa M, Dai D, Kubo S, Black C, Peri K, McAlear TS, Veyron S, Yang SK, Vargas J, Bechstedt S, Trempe JF, Bui KH
eLife (2020) 9 [ Pubmed: 31951202 DOI: doi:10.7554/eLife.52760 ]
- Tubulin beta (49 kDa, Protein from Chlamydomonas reinhardtii)
- Fap276 (10 kDa, Protein from Chlamydomonas reinhardtii)
- Cilia- and flagella-associated protein 20 (22 kDa, Protein from Chlamydomonas reinhardtii)
- Fap52 (68 kDa, Protein from Chlamydomonas reinhardtii)
- Tubulin alpha (49 kDa, Protein from Chlamydomonas reinhardtii)
- Inner junction complex of the cilia (1 MDa, Cellular component from Chlamydomonas reinhardtii)
- Flagellar associated protein (27 kDa, Protein from Chlamydomonas reinhardtii)
- Protein flattop homolog (15 kDa, Protein from Chlamydomonas reinhardtii)
- Pacrg (34 kDa, Protein from Chlamydomonas reinhardtii)
48-nm repeat unit of the doublet microtubule from Chlamydomonas reinhardtii
Resolution: 4.57 Å
EM Method: Single-particle
Fitted PDBs: 6ve7
Q-score: 0.028
Khalifa AAZ, Ichikawa M, Dai D, Kubo S, Black C, Peri K, McAlear TS, Veyron S, Yang SK, Vargas J, Bechstedt S, Trempe JF, Bui KH
eLife (2020) 9 [ Pubmed: 31951202 DOI: doi:10.7554/eLife.52760 ]
16-nm repeat of the doublet microtubule from Tetrahymena thermophila
Khalifa AAZ, Ichikawa M, Dai D, Kubo S, Black C, Peri K, McAlear TS, Veyron S, Yang SK, Vargas J, Bechstedt S, Trempe JF, Bui KH
eLife (2020) 9 [ Pubmed: 31951202 DOI: doi:10.7554/eLife.52760 ]
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 alpha chain (49 kDa, Protein from Tetrahymena thermophila)
- Magnesium ion (24 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 48nm-repeat of microtubule doublet (Cellular component from Tetrahymena thermophila)
- Tubulin beta chain (49 kDa, Protein from Tetrahymena thermophila)
Cryo-EM map of the A-tubule prepared by sonication
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 ]