Cryo-EM structure of SAM-Tom40 intermediate complex
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7vku
Q-score: 0.509
Takeda H, Busto JV, Lindau C, Tsutsumi A, Tomii K, Imai K, Yamamori Y, Hirokawa T, Motono C, Ganesan I, Wenz LS, Becker T, Kikkawa M, Pfanner N, Wiedemann N, Endo T
Nat Struct Mol Biol (2023) 30 pp. 233-233 [ DOI: doi:10.1038/s41594-023-00926-8 Pubmed: 36697808 ]
- Mitochondrial import receptor subunit tom40 (42 kDa, Protein from Saccharomyces cerevisiae S288C)
- Sam-tom40 (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Sorting assembly machinery 35 kda subunit (37 kDa, Protein from Saccharomyces cerevisiae S288C)
- Sorting assembly machinery 37 kda subunit (37 kDa, Protein from Saccharomyces cerevisiae S288C)
- Sorting assembly machinery 50 kda subunit (54 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7w7t
Q-score: 0.431
Zhang Y, Kobayashi C, Cai X, Watanabe S, Tsutsumi A, Kikkawa M, Sugita Y, Inaba K
Cell Rep (2022) 41 pp. 111760-111760 [ DOI: doi:10.1016/j.celrep.2022.111760 Pubmed: 36476867 ]
- Serca2b with ca (110 MDa, Complex from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Sarcoplasmic/endoplasmic reticulum calcium atpase 2 (114 kDa, Protein from Homo sapiens)
The 'Ca2+-unbound' BeF3- of SERCA2b
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7w7u
Q-score: 0.52
Zhang Y, Kobayashi C, Cai X, Watanabe S, Tsutsumi A, Kikkawa M, Sugita Y, Inaba K
Cell Rep (2022) 41 pp. 111760-111760 [ DOI: doi:10.1016/j.celrep.2022.111760 Pubmed: 36476867 ]
- Serca2b with ca (110 MDa, Complex from Homo sapiens)
- Sarcoplasmic/endoplasmic reticulum calcium atpase 2 (114 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7w7v
Q-score: 0.473
Zhang Y, Kobayashi C, Cai X, Watanabe S, Tsutsumi A, Kikkawa M, Sugita Y, Inaba K
Cell Rep (2022) 41 pp. 111760-111760 [ DOI: doi:10.1016/j.celrep.2022.111760 Pubmed: 36476867 ]
- Serca2b with ca (110 MDa, Complex from Homo sapiens)
- Sarcoplasmic/endoplasmic reticulum calcium atpase 2 (114 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7w7w
Q-score: 0.482
Zhang Y, Kobayashi C, Cai X, Watanabe S, Tsutsumi A, Kikkawa M, Sugita Y, Inaba K
Cell Rep (2022) 41 pp. 111760-111760 [ DOI: doi:10.1016/j.celrep.2022.111760 Pubmed: 36476867 ]
- Serca2b with ca (110 MDa, Complex from Homo sapiens)
- Sarcoplasmic/endoplasmic reticulum calcium atpase 2 (114 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Tetrafluoroaluminate ion (102 Da, Ligand)
Structure of recombinant RyR2 mutant K4593A (EGTA dataset)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7vmr
Q-score: 0.362
Kobayashi T, Tsutsumi A, Kurebayashi N, Saito K, Kodama M, Sakurai T, Kikkawa M, Murayama T, Ogawa H
Nat Commun (2022) 13 pp. 2821-2821 [ DOI: doi:10.1038/s41467-022-30429-x Pubmed: 35595836 ]
- Peptidyl-prolyl cis-trans isomerase fkbp1b (18 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ryanodine receptor 2 (533 kDa, Protein from Mus musculus)
- Recombinant ryr2 mutant k4593a in the presence of egta (Complex from Mus musculus)
- Ryanodine receptor 2 (Complex from Homo sapiens)
- Fkbp1b (Complex)
Structure of recombinant RyR2 mutant K4593A (Ca2+ dataset)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7vms
Q-score: 0.299
Kobayashi T, Tsutsumi A, Kurebayashi N, Saito K, Kodama M, Sakurai T, Kikkawa M, Murayama T, Ogawa H
Nat Commun (2022) 13 pp. 2821- [ DOI: doi:10.1038/s41467-022-30429-x ]
- Peptidyl-prolyl cis-trans isomerase fkbp1b (18 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Recombinant ryr2 mutant k4593a in the presence of ca2+ (Cell from Mus musculus)
- Ryanodine receptor 2 (533 kDa, Protein from Mus musculus)
Cryo-EM structure of human XKR8-basigin complex bound to Fab fragment
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7dce
Q-score: 0.423
Sakuragi T, Kanai R, Tsutsumi A, Narita H, Onishi E, Nishino K, Miyazaki T, Baba T, Kosako H, Nakagawa A, Kikkawa M, Toyoshima C, Nagata S
Nat Struct Mol Biol (2021) 28 pp. 825-834 [ Pubmed: 34625749 DOI: doi:10.1038/s41594-021-00665-8 ]
- Human xkr8-basigin complex (Complex from Homo sapiens)
- 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (782 Da, Ligand)
- Light chain of fab fragment (23 kDa, Protein from Oryctolagus cuniculus)
- Fab fragment (Complex from Oryctolagus cuniculus)
- Human xkr8-basigin complex bound to fab fragment (110 kDa, Complex)
- Heavy chain of fab fragment (22 kDa, Protein from Oryctolagus cuniculus)
- Xk-related protein 8 (45 kDa, Protein from Homo sapiens)
- Isoform 2 of basigin (19 kDa, Protein from Homo sapiens)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7e7s
Q-score: 0.472
Zhang Y, Watanabe S, Tsutsumi A, Kadokura H, Kikkawa M, Inaba K
EMBO J (2021) 40 pp. e108482-e108482 [ DOI: doi:10.15252/embj.2021108482 Pubmed: 34459010 ]
- Serca2b with ca (110 MDa, Complex from Homo sapiens)
- Sarcoplasmic/endoplasmic reticulum calcium atpase 2 (114 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
The mitochondrial SAM-Mdm10 supercomplex in Nanodisc from S.cere
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7bty
Q-score: 0.533
Takeda H, Tsutsumi A, Nishizawa T, Lindau C, Busto JV, Wenz LS, Ellenrieder L, Imai K, Straub SP, Mossmann W, Qiu J, Yamamori Y, Tomii K, Suzuki J, Murata T, Ogasawara S, Nureki O, Becker T, Pfanner N, Wiedemann N, Kikkawa M, Endo T
Nature (2021) 590 pp. 163-169 [ DOI: doi:10.1038/s41586-020-03113-7 Pubmed: 33408415 ]
- Sam-mdm10 complex (Complex from Saccharomyces cerevisiae)
- Mitochondrial outer membrane beta-barrel protein (41 kDa, Protein from Saccharomyces cerevisiae)
- Sorting assembly machinery 35 kda subunit (37 kDa, Protein from Saccharomyces cerevisiae)
- Sorting assembly machinery 37 kda subunit (37 kDa, Protein from Saccharomyces cerevisiae)
- Mdm10 isoform 1 (56 kDa, Protein from Saccharomyces cerevisiae)