Structure of Eastern Equine Encephalitis VLP in complex with the receptor VLDLR LA1-2
Cao D, Ma B, Cao Z, Xu X, Zhang X, Xiang Y
Nat Commun (2024) 15 pp. 6866-6866 [ Pubmed: 39127734 DOI: doi:10.1038/s41467-024-51293-x ]
- Calcium ion (40 Da, Ligand)
- Spike glycoprotein e1 (47 kDa, Protein from Eastern equine encephalitis virus)
- Spike glycoprotein e2 (47 kDa, Protein from Eastern equine encephalitis virus)
- Very low-density lipoprotein receptor (9 kDa, Protein from Homo sapiens)
- Capsid protein (29 kDa, Protein from Eastern equine encephalitis virus)
- East equine encephalitis virus vlp in complex with its receptor vldlr la1-2 at the asymmetric unit (Complex from Eastern equine encephalitis virus)
Structure of Eastern Equine Encephalitis VLP in complex with the receptor VLDLR LA3-5
Cao D, Ma B, Cao Z, Xu X, Zhang X, Xiang Y
Nat Commun (2024) 15 pp. 6866-6866 [ Pubmed: 39127734 DOI: doi:10.1038/s41467-024-51293-x ]
- East equine encephalitis virus vlp in complex with its receptor vldlr la3-5 at the asymmetric unit (Complex from Eastern equine encephalitis virus)
- Very low-density lipoprotein receptor (4 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Spike glycoprotein e1 (47 kDa, Protein from Eastern equine encephalitis virus)
- Spike glycoprotein e2 (47 kDa, Protein from Eastern equine encephalitis virus)
- Capsid protein (29 kDa, Protein from Eastern equine encephalitis virus)
- Very low-density lipoprotein receptor (4 kDa, Protein from Homo sapiens)
Post-fusion structure of SARS-CoV spike glycoprotein
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6m3w
Q-score: 0.366
Nat Commun (2020) 11 pp. 3618-3618 [ DOI: doi:10.1038/s41467-020-17371-6 Pubmed: 32681106 ]
Supercomplex for cylic electron transport in cyanobacteria
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6khi
Q-score: 0.525
Pan X, Cao D, Xie F, Xu F, Su X, Mi H, Zhang X, Li M
Nat Commun (2020) 11 pp. 610-610 [ Pubmed: 32001694 DOI: doi:10.1038/s41467-020-14456-0 ]
- Nadh dehydrogenase subunit 5 (72 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Tlr0472 protein (16 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Ferredoxin-1 (10 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Nad(p)h-quinone oxidoreductase subunit j (19 kDa, Protein from Thermosynechococcus elongatus BP-1)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit l (8 kDa, Protein from Thermosynechococcus elongatus BP-1)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit m (12 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Nad(p)h-quinone oxidoreductase subunit n (16 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit i (22 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Nad(p)h-quinone oxidoreductase subunit k (25 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Nad(p)h-quinone oxidoreductase chain 4 1 (57 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nad(p)h-quinone oxidoreductase subunit 4l (11 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Nad(p)h-quinone oxidoreductase subunit 1 (40 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Proton-translocating nadh-quinone dehydrogenase subunit p (4 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Nad(p)h-quinone oxidoreductase subunit h (45 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Nad(p)h-quinone oxidoreductase subunit o (7 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nad(p)h-quinone oxidoreductase subunit 2 (55 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Tlr0636 protein (12 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Iron/sulfur cluster (351 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit 3 (15 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Nadh-quinone oxidoreductase subunit j (21 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Proton-translocating nadh-quinone dehydrogenase subunit q (4 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Beta-carotene (536 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Electron transport complex ndh-fd from cyanobacteria (Complex from Thermosynechococcus elongatus BP-1)
Supercomplex for electron transfer
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6khj
Q-score: 0.562
Pan X, Cao D, Xie F, Xu F, Su X, Mi H, Zhang X, Li M
Nat Commun (2020) 11 pp. 610-610 [ DOI: doi:10.1038/s41467-020-14456-0 Pubmed: 32001694 ]
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Proton-translocating nadh-quinone dehydrogenase subunit p (4 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Nad(p)h-quinone oxidoreductase subunit h (45 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Nad(p)h-quinone oxidoreductase subunit 2 (55 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Nad(p)h-quinone oxidoreductase subunit n (16 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Proton-translocating nadh-quinone dehydrogenase subunit q (4 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Cylic electron transfer supercomplex from cyanobacteria (Complex from Thermosynechococcus elongatus BP-1)
- Iron/sulfur cluster (351 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit 3 (15 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit k (25 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Nadh dehydrogenase subunit 5 (72 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Tlr0636 protein (12 kDa, Protein from Thermosynechococcus elongatus BP-1)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit j (19 kDa, Protein from Thermosynechococcus elongatus BP-1)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit l (8 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Nad(p)h-quinone oxidoreductase subunit 1 (40 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Nad(p)h-quinone oxidoreductase subunit o (7 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Nad(p)h-quinone oxidoreductase subunit i (22 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Beta-carotene (536 Da, Ligand)
- Nadh-quinone oxidoreductase subunit j (21 kDa, Protein from Thermosynechococcus elongatus BP-1)
- 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone (749 Da, Ligand)
- Nad(p)h-quinone oxidoreductase chain 4 1 (57 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Nad(p)h-quinone oxidoreductase subunit m (12 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Nad(p)h-quinone oxidoreductase subunit 4l (11 kDa, Protein from Thermosynechococcus elongatus BP-1)
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 reaction center subunit iii (17 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 ii (15 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)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i-isia-flavodoxin supercomplex (Complex from Synechococcus elongatus PCC 7942)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i iron-sulfur center (8 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Psam (3 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i reaction center subunit xi (17 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Water (18 Da, Ligand)
- Flavodoxin (18 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Flavin mononucleotide (456 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i reaction center subunit ix (4 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit psak (8 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Phylloquinone (450 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Iron stress-induced chlorophyll-binding protein (37 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
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 [ Pubmed: 32042157 DOI: doi:10.1038/s41477-020-0593-7 ]
- Photosystem i reaction center subunit ii (15 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Psam (3 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i reaction center subunit psak (8 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i psai protein (4 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Iron stress-induced chlorophyll-binding protein (37 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i p700 chlorophyll a apoprotein a2 (81 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))
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Water (18 Da, Ligand)
- Photosystem i iron-sulfur center (8 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)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Chlorophyll a (893 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit xi (17 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
Prefusion structure of SARS-CoV spike glycoprotein, conformation 1
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 5x58
Q-score: 0.409
Yuan Y, Cao D, Zhang Y, Ma J, Qi J, Wang Q, Lu G, Wu Y, Yan J, Shi Y, Zhang X, Gao GF
Nat Commun (2017) 8 pp. 15092-15092 [ DOI: doi:10.1038/ncomms15092 Pubmed: 28393837 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (136 kDa, Protein from SARS coronavirus BJ01)
- Sars-cov spike trimer (Complex from SARS coronavirus BJ01)
Prefusion structure of SARS-CoV spike glycoprotein, conformation 2
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 5x5b
Q-score: 0.333
Yuan Y, Cao D, Zhang Y, Ma J, Qi J, Wang Q, Lu G, Wu Y, Yan J, Shi Y, Zhang X, Gao GF
Nat Commun (2017) 8 pp. 15092-15092 [ DOI: doi:10.1038/ncomms15092 Pubmed: 28393837 ]
- Spike glycoprotein (136 kDa, Protein from SARS coronavirus BJ01)
- Sars-cov spike trimer (Complex from SARS coronavirus BJ01)