Local refined cryo-EM reconstruction of Omicron BA.5 RBD in complex with 8-9D Fab
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8j1t
Q-score: 0.455
Tai W, Yang K, Liu Y, Li R, Feng S, Chai B, Zhuang X, Qi S, Shi H, Liu Z, Lei J, Ma E, Wang W, Tian C, Le T, Wang J, Chen Y, Tian M, Xiang Y, Yu G, Cheng G
Nat Commun (2023) 14 pp. 8042-8042 [ DOI: doi:10.1038/s41467-023-43798-8 Pubmed: 38052844 ]
- Severe acute respiratory syndrome coronavirus 2 omicron ba.5 rbd bound 8-9d fab (22 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov2 omicron ba.5 rbd (Complex)
- 8-9d heavy chain (12 kDa, Protein from Homo sapiens)
- 8-9d light chain (11 kDa, Protein from Homo sapiens)
- 8-9d fab (Complex from Homo sapiens)
- Spike protein (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM reconstruction of SARS-CoV2 Omicron BA.5 spike in complex with 8-9D Fabs
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 8j1v
Q-score: 0.374
Tai W, Yang K, Liu Y, Li R, Feng S, Chai B, Zhuang X, Qi S, Shi H, Liu Z, Lei J, Ma E, Wang W, Tian C, Le T, Wang J, Chen Y, Tian M, Xiang Y, Yu G, Cheng G
Nat Commun (2023) 14 pp. 8042-8042 [ DOI: doi:10.1038/s41467-023-43798-8 Pubmed: 38052844 ]
- Sars-cov2 omicron ba.5 spike ectodomain (Complex)
- 8-9d heavy chain (12 kDa, Protein from Homo sapiens)
- Severe acute respiratory syndrome coronavirus 2 omicron ba.5 spike bound 8-9d fab (369 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- 8-9d light chain (11 kDa, Protein from Homo sapiens)
- Spike protein s2' (123 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 8-9d fab variable region (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 3.17 Å
EM Method: Single-particle
Fitted PDBs: 7ml7
Q-score: 0.516
Chen P, Zeng J, Liu Z, Thaker H, Wang S, Tian S, Zhang J, Tao L, Gutierrez CB, Xing L, Gerhard R, Huang L, Dong M, Jin R
Nat Commun (2021) 12 pp. 3748-3748 [ Pubmed: 34145250 DOI: doi:10.1038/s41467-021-23878-3 ]
- Em map of tcdb in complex with cspg4 (Complex)
- Cspg4 (Complex from Homo sapiens)
- Tcdb (Complex from Clostridioides difficile)
- Chondroitin sulfate proteoglycan 4 (82 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Toxin b (228 kDa, Protein from Clostridioides difficile)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7d74
Q-score: 0.394
Zheng L, Liu Z, Wang Y, Yang F, Wang J, Huang W, Qin J, Tian M, Cai X, Liu X, Mo X, Gao N, Jia D
Nat Struct Mol Biol (2021) 28 pp. 1-12 [ DOI: doi:10.1038/s41594-021-00591-9 Pubmed: 33986552 ]
- Mannose-1-phosphate guanyltransferase beta (39 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Mannose-1-phosphate guanyltransferase alpha (46 kDa, Protein from Homo sapiens)
- Complex (Complex from Homo sapiens)
Cryo-EM structures of human GMPPA/GMPPB complex bound to GDP-Mannose
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7d72
Q-score: 0.444
Zheng L, Liu Z, Wang Y, Yang F, Wang J, Huang W, Qin J, Tian M, Cai X, Liu X, Mo X, Gao N, Jia D
Nat Struct Mol Biol (2021) 28 pp. 1-12 [ DOI: doi:10.1038/s41594-021-00591-9 Pubmed: 33986552 ]
- Gmppa/gmppb complex (Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Mannose-1-phosphate guanyltransferase beta (39 kDa, Protein from Homo sapiens)
- Mannose-1-phosphate guanyltransferase alpha (46 kDa, Protein from Homo sapiens)
- Guanosine-5'-diphosphate-alpha-d-mannose (605 Da, Ligand)
Cryo-EM structure of GMPPA/GMPPB complex bound to GTP (State I)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7d73
Q-score: 0.515
Zheng L, Liu Z, Wang Y, Yang F, Wang J, Huang W, Qin J, Tian M, Cai X, Liu X, Mo X, Gao N, Jia D
Nat Struct Mol Biol (2021) 28 pp. 1-12 [ DOI: doi:10.1038/s41594-021-00591-9 Pubmed: 33986552 ]
- Mannose-1-phosphate guanyltransferase beta (39 kDa, Protein from Homo sapiens)
- Mannose-1-phosphate guanyltransferase alpha (46 kDa, Protein from Homo sapiens)
- Guanosine-5'-diphosphate-alpha-d-mannose (605 Da, Ligand)
- Complex (Complex from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
Structure of cyanobacterial photosystem I-IsiA-flavodoxin supercomplex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6kif
Q-score: 0.36
Cao P, Cao D, Si L, Su X, Tian L, Chang W, Liu Z, Zhang X, Li M
Nat Plants (2020) 6 pp. 167-176 [ DOI: doi:10.1038/s41477-020-0593-7 Pubmed: 32042157 ]
- Photosystem i iron-sulfur center (8 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i reaction center subunit iv (8 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i reaction center subunit psak (8 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i reaction center subunit xi (17 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Beta-carotene (536 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Psam (3 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i reaction center subunit iii (17 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Photosystem i-isia-flavodoxin supercomplex (Complex from Synechococcus elongatus PCC 7942)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Iron stress-induced chlorophyll-binding protein (37 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Water (18 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Flavodoxin (18 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i psai protein (4 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i reaction center subunit ix (4 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
Structure of cyanobacterial photosystem I-IsiA supercomplex
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6kig
Q-score: 0.419
Cao P, Cao D, Si L, Su X, Tian L, Chang W, Liu Z, Zhang X, Li M
Nat Plants (2020) 6 pp. 167-176 [ DOI: doi:10.1038/s41477-020-0593-7 Pubmed: 32042157 ]
- Photosystem i iron-sulfur center (8 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i-isia supercomplex (Complex from Synechococcus elongatus PCC 7942)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i reaction center subunit psak (8 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i reaction center subunit xi (17 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Beta-carotene (536 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Psam (3 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i reaction center subunit iii (17 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Iron stress-induced chlorophyll-binding protein (37 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Water (18 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i psai protein (4 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i reaction center subunit ix (4 kDa, Protein from Synechococcus elongatus (strain PCC 7942))