open state RyR2 in detergent in complex with nanobody
Li C, Willegems K, Uchanski T, Pardon E, Steyaert J, Efremov RG
J Biol Chem (2024) 300 pp. 107734-107734 [ Pubmed: 39233227 DOI: doi:10.1016/j.jbc.2024.107734 ]
TM part of RyR2 in detergent in open state
Li C, Willegems K, Uchanski T, Pardon E, Steyaert J, Efremov RG
J Biol Chem (2024) 300 pp. 107734-107734 [ Pubmed: 39233227 DOI: doi:10.1016/j.jbc.2024.107734 ]
Cryo-EM structure of the CRT-LESS RC-LH core complex from roseiflexus castenholzii
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8iun
Q-score: 0.613
Qi CH, Wang GL, Wang FF, Xin Y, Zou MJ, Madigan MT, Wang-Otomo ZY, Ma F, Yu LJ
J Biol Chem (2023) 299 pp. 105057-105057 [ Pubmed: 37468106 DOI: doi:10.1016/j.jbc.2023.105057 ]
- Bacteriochlorophyll a (911 Da, Ligand)
- Cytochrome subunit of photosynthetic reaction center (34 kDa, Protein from Roseiflexus castenholzii)
- Manganese (ii) ion (54 Da, Ligand)
- Reaction center protein l chain (71 kDa, Protein from Roseiflexus castenholzii)
- 2-o-octyl-beta-d-glucopyranose (292 Da, Ligand)
- Heme c (618 Da, Ligand)
- Antenna complex alpha/beta subunit (6 kDa, Protein from Roseiflexus castenholzii)
- Unknown ligand (691 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii)
- Bacteriopheophytin a (889 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Reaction center unknown polypeptide (740 Da, Protein from Roseiflexus castenholzii)
- Gamma-carotene (536 Da, Ligand)
- Reaction center small polypeptide (4 kDa, Protein from Roseiflexus castenholzii)
- Calcium ion (40 Da, Ligand)
- Reaction center small polypeptide (6 kDa, Protein from Roseiflexus castenholzii)
- 2-methyl-3-[(2e,6e,10e,14e,18e,22e,26e,30e,34e,38e)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione (921 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Crt-less rc-lh core complex (Complex from Roseiflexus castenholzii)
Cryo-EM structure of the RC-LH core complex from roseiflexus castenholzii
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 8iug
Q-score: 0.622
Qi CH, Wang GL, Wang FF, Xin Y, Zou MJ, Madigan MT, Wang-Otomo ZY, Ma F, Yu LJ
J Biol Chem (2023) 299 pp. 105057-105057 [ Pubmed: 37468106 DOI: doi:10.1016/j.jbc.2023.105057 ]
- Bacteriochlorophyll a (911 Da, Ligand)
- Unknown ligand (Ligand)
- Cytochrome subunit of photosynthetic reaction center (34 kDa, Protein from Roseiflexus castenholzii)
- Manganese (ii) ion (54 Da, Ligand)
- Reaction center protein l chain (71 kDa, Protein from Roseiflexus castenholzii)
- 2-o-octyl-beta-d-glucopyranose (292 Da, Ligand)
- Heme c (618 Da, Ligand)
- Antenna complex alpha/beta subunit (6 kDa, Protein from Roseiflexus castenholzii)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii)
- Bacteriopheophytin a (889 Da, Ligand)
- [(2~{r},3~{s},4~{s},5~{r},6~{r})-6-[(6~{e},8~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{e},24~{e})-2,6,10,14,19,23-hexamethyl-25-(2,6,6-trimethylcyclohexen-1-yl)pentacosa-6,8,10,12,14,16,18,20,22,24-decaen-2-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methyl pentadecanoate (941 Da, Ligand)
- Tmx polypeptide (3 kDa, Protein from Roseiflexus castenholzii)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Rc-lh core complex (Complex from Roseiflexus castenholzii)
- Reaction center unknown polypeptide (740 Da, Protein from Roseiflexus castenholzii)
- Gamma-carotene (536 Da, Ligand)
- Reaction center small polypeptide (4 kDa, Protein from Roseiflexus castenholzii)
- Calcium ion (40 Da, Ligand)
- Reaction center small polypeptide (6 kDa, Protein from Roseiflexus castenholzii)
- 2-methyl-3-[(2e,6e,10e,14e,18e,22e,26e,30e,34e,38e)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione (921 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF Allochromatium tepidum
Resolution: 2.81 Å
EM Method: Single-particle
Fitted PDBs: 7vrj
Q-score: 0.601
Tani K, Kobayashi K, Hosogi N, Ji XC, Nagashima S, Nagashima KVP, Izumida A, Inoue K, Tsukatani Y, Kanno R, Hall M, Yu LJ, Ishikawa I, Okura Y, Madigan MT, Mizoguchi A, Humbel BM, Kimura Y, Wang-Otomo ZY
J Biol Chem (2022) 298 pp. 101967-101967 [ DOI: doi:10.1016/j.jbc.2022.101967 Pubmed: 35460693 ]
- Light-harvesting protein lh1 alpha1 (7 kDa, Protein from Allochromatium tepidum)
- Bacteriochlorophyll a (911 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)
- Heme c (618 Da, Ligand)
- Light-harvesting protein lh1 beta3 (5 kDa, Protein from Allochromatium tepidum)
- Photosynthetic reaction center cytochrome c subunit (43 kDa, Protein from Allochromatium tepidum)
- Light-harvesting protein lh1 alpha3 (7 kDa, Protein from Allochromatium tepidum)
- Bacteriopheophytin a (889 Da, Ligand)
- Light-harvesting protein lh1 beta1 (5 kDa, Protein from Allochromatium tepidum)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Water (18 Da, Ligand)
- Photosynthetic reaction center h subunit (28 kDa, Protein from Allochromatium tepidum)
- Photosynthetic lh1-rc complex from the purple phototrophic bacterium allochromatium tepidum (Complex from Allochromatium tepidum)
- Palmitic acid (256 Da, Ligand)
- Light-harvesting protein lh1 alpha2 (5 kDa, Protein from Allochromatium tepidum)
- Magnesium ion (24 Da, Ligand)
- Photosynthetic reaction center l subunit (31 kDa, Protein from Allochromatium tepidum)
- Ubiquinone-8 (727 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Photosynthetic reaction center m subunit (36 kDa, Protein from Allochromatium tepidum)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Diacyl glycerol (625 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7vsg
Q-score: 0.434
Nakanishi H, Hayashida K, Nishizawa T, Oshima A, Abe K
J Biol Chem (2022) 298 pp. 101498-101498 [ DOI: doi:10.1016/j.jbc.2021.101498 Pubmed: 34922944 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Phospholipid-transporting atpase ig (124 kDa, Protein from Homo sapiens)
- Cryo-em structure of a human atp11c-cdc50a flippase reconstituted in the nanodisc in ptdser-occluded e2-pi state. (Complex from Homo sapiens)
- O-[(s)-({(2r)-2,3-bis[(9z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-l-serine (788 Da, Ligand)
- Cell cycle control protein 50a (40 kDa, Protein from Homo sapiens)
Cryo-EM structure of a human ATP11C-CDC50A flippase reconstituted in the Nanodisc in E1P state.
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7vsh
Q-score: 0.513
Nakanishi H, Hayashida K, Nishizawa T, Oshima A, Abe K
J Biol Chem (2022) 298 pp. 101498-101498 [ DOI: doi:10.1016/j.jbc.2021.101498 Pubmed: 34922944 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cryo-em structure of a human atp11c-cdc50a flippase reconstituted in the nanodisc in e1p state. (Complex from Homo sapiens)
- O-[(s)-({(2r)-2,3-bis[(9z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-l-serine (788 Da, Ligand)
- Phospholipid-transporting atpase ig (124 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Cell cycle control protein 50a (40 kDa, Protein from Homo sapiens)
- Tetrafluoroaluminate ion (102 Da, Ligand)