Cryo-EM structure of STING oligomer bound to cGAMP and NVS-STG2
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8flk
Q-score: 0.438
Li J, Canham SM, Wu H, Henault M, Chen L, Liu G, Chen Y, Yu G, Miller HR, Hornak V, Brittain SM, Michaud GA, Tutter A, Broom W, Digan ME, McWhirter SM, Sivick KE, Pham HT, Chen CH, Tria GS, McKenna JM, Schirle M, Mao X, Nicholson TB, Wang Y, Jenkins JL, Jain RK, Tallarico JA, Patel SJ, Zheng L, Ross NT, Cho CY, Zhang X, Bai XC, Feng Y
Nat Chem Biol (2024) 20 pp. 365-372 [ Pubmed: 37828400 DOI: doi:10.1038/s41589-023-01434-y ]
- Sting tetramer (300 kDa, Complex from Homo sapiens)
- Cgamp (674 Da, Ligand)
- 4-({[4-(2-tert-butyl-5,5-dimethyl-1,3-dioxan-2-yl)phenyl]methyl}amino)-3-methoxybenzoic acid (427 Da, Ligand)
- Stimulator of interferon genes protein (39 kDa, Protein from Homo sapiens)
PSI-NDH supercomplex of Barley
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7f9o
Q-score: 0.153
Shen L, Tang K, Wang W, Wang C, Wu H, Mao Z, An S, Chang S, Kuang T, Shen JR, Han G, Zhang X
Nature (2022) 601 pp. 649-654 [ Pubmed: 34879391 DOI: doi:10.1038/s41586-021-04277-6 ]
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex b5 (18 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit iv, chloroplastic (15 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit ii, chloroplastic (21 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein, chloroplastic (27 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex b1 (51 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Beta-carotene (536 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit xi, chloroplastic (22 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit psak, chloroplastic (13 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-beta,beta-carotene-3,3'-diol (600 Da, Ligand)
- Photosynthetic ndh subunit of subcomplex l2 (24 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Unidentified stromal protein (5 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex l1 (17 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex b3 (13 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex l4 (13 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Psi-ndh supercomplex of barley (Complex from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein lhca5 (27 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit 1, chloroplastic (38 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein lhca1 (26 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit m, chloroplastic (24 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein, chloroplastic (29 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit n, chloroplastic (25 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit 6, chloroplastic (19 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex l5 (25 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit 2, chloroplastic (53 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Phylloquinone (450 Da, Ligand)
- Chlorophyll a-b binding protein lhca4 (21 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit vi, chloroplastic (14 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex b4 (9 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit h, chloroplastic (44 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- 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 j, chloroplastic (18 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a (893 Da, Ligand)
- Photosynthetic ndh subunit of subcomplex b2 (38 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit i, chloroplastic (19 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit iii, chloroplastic (24 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit 3, chloroplastic (13 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit k, chloroplastic (27 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase chain 4, chloroplastic (56 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit l, chloroplastic (22 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex l2 (23 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Iron/sulfur cluster (351 Da, Ligand)
- Nadh-plastoquinone oxidoreductase subunit 5 (87 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit 4l, chloroplastic (11 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a isomer (893 Da, Ligand)
Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 6dbo
Q-score: 0.297
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H
Nat Struct Mol Biol (2018) 25 pp. 732-742 [ DOI: doi:10.1038/s41594-018-0098-5 Pubmed: 30061602 ]
- Rag in complex with 12-rss and 23-rss substrate dnas (Complex from Danio rerio)
- Recombination activating gene 1 - mbp chimera (131 kDa, Protein from Danio rerio)
- Reverse strand of substrate rss dna (9 kDa, DNA from Danio rerio)
- Zinc ion (65 Da, Ligand)
- Forward strand of substrate rss dna (9 kDa, DNA from Danio rerio)
- Recombination activating gene 2 (59 kDa, Protein from Danio rerio)
- Calcium ion (40 Da, Ligand)
Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs
Resolution: 4.22 Å
EM Method: Single-particle
Fitted PDBs: 6dbq
Q-score: 0.296
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H
Nat Struct Mol Biol (2018) 25 pp. 732-742 [ DOI: doi:10.1038/s41594-018-0098-5 Pubmed: 30061602 ]
- Rag in complex with 12-rss and 23-rss substrate dnas (Complex from Danio rerio)
- Molecule name: reverse strand of 12-rss substrate dna (15 kDa, DNA from Danio rerio)
- Reverse strand of 23-rss substrate dna (18 kDa, DNA from Danio rerio)
- Recombination activating gene 1 - mbp chimera (131 kDa, Protein from Danio rerio)
- Zinc ion (65 Da, Ligand)
- Recombination activating gene 2 (59 kDa, Protein from Danio rerio)
- Calcium ion (40 Da, Ligand)
- Molecule name: forward strand of 12-rss substrate dna (15 kDa, DNA from Danio rerio)
- Molecule name: forward strand of 23-rss substrate dna (18 kDa, DNA from Danio rerio)
Cryo-EM structure of RAG in complex with one melted RSS and one unmelted RSS
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6dbr
Q-score: 0.36
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H
Nat Struct Mol Biol (2018) 25 pp. 732-742 [ DOI: doi:10.1038/s41594-018-0098-5 Pubmed: 30061602 ]
- Reverse strand of unmelted rss substrate dna (10 kDa, DNA from Danio rerio)
- Forward strand of unmelted rss substrate dna (10 kDa, DNA from Danio rerio)
- Recombination activating gene 1 - mbp chimera (131 kDa, Protein from Danio rerio)
- Zinc ion (65 Da, Ligand)
- Recombination activating gene 2 (59 kDa, Protein from Danio rerio)
- Rag in complex with one melted rss and one unmelted rss (Complex from Danio rerio)
- Calcium ion (40 Da, Ligand)
- Reverse strand of melted rss substrate dna (10 kDa, DNA from Danio rerio)
- Forward strand of melted rss substrate dna (10 kDa, DNA from Danio rerio)
Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 6dbt
Q-score: 0.323
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H
Nat Struct Mol Biol (2018) 25 pp. 732-742 [ DOI: doi:10.1038/s41594-018-0098-5 Pubmed: 30061602 ]
- Rag in complex with 12-rss and 23-rss substrate dnas (Complex from Danio rerio)
- Reverse strand of 23-rss substrate dna (18 kDa, DNA from Danio rerio)
- Recombination activating gene 1 - mbp chimera (131 kDa, Protein from Danio rerio)
- Reverse strand of 12-rss substrate dna (15 kDa, DNA from Danio rerio)
- Zinc ion (65 Da, Ligand)
- Recombination activating gene 2 (59 kDa, Protein from Danio rerio)
- Calcium ion (40 Da, Ligand)
- Forward strand of 23-rss substrate dna (18 kDa, DNA from Danio rerio)
- Forward strand of 12-rss substrate dna (15 kDa, DNA from Danio rerio)
Cryo-EM structure of RAG in complex with melted 12-RSS and unmelted 23-RSS substrates
Resolution: 4.29 Å
EM Method: Single-particle
Fitted PDBs: 6dbv
Q-score: 0.296
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H
Nat Struct Mol Biol (2018) 25 pp. 732-742 [ DOI: doi:10.1038/s41594-018-0098-5 Pubmed: 30061602 ]
- Rag in complex with 12-rss and 23-rss substrate dnas (Complex from Danio rerio)
- Reverse strand of 23-rss substrate dna (18 kDa, DNA from Danio rerio)
- Recombination activating gene 1 - mbp chimera (131 kDa, Protein from Danio rerio)
- Reverse strand of 12-rss substrate dna (15 kDa, DNA from Danio rerio)
- Zinc ion (65 Da, Ligand)
- Recombination activating gene 2 (59 kDa, Protein from Danio rerio)
- Calcium ion (40 Da, Ligand)
- Forward strand of 23-rss substrate dna (18 kDa, DNA from Danio rerio)
- Forward strand of 12-rss substrate dna (15 kDa, DNA from Danio rerio)
- Recombination activating gene 1 - mbp chimera (131 kDa, Protein from Danio rerio)
Cryo-EM structure of RAG in complex with 12-RSS substrate DNA
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 6dbw
Q-score: 0.265
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H
Nat Struct Mol Biol (2018) 25 pp. 732-742 [ DOI: doi:10.1038/s41594-018-0098-5 Pubmed: 30061602 ]
- Rag in complex with 12-rss substrate dna (Complex from Danio rerio)
- Recombination activating gene 1 - mbp chimera (131 kDa, Protein from Danio rerio)
- Reverse strand of 12-rss substrate dna (15 kDa, DNA from Danio rerio)
- Zinc ion (65 Da, Ligand)
- Recombination activating gene 2 (59 kDa, Protein from Danio rerio)
- Calcium ion (40 Da, Ligand)
- Forward strand of 12-rss substrate dna (15 kDa, DNA from Danio rerio)
Cryo-EM structure of RAG in complex with 12-RSS substrate DNA
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 6dbx
Q-score: 0.307
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H
Nat Struct Mol Biol (2018) 25 pp. 732-742 [ DOI: doi:10.1038/s41594-018-0098-5 Pubmed: 30061602 ]
- Rag in complex with 12-rss substrate dna (Complex from Danio rerio)
- Recombination activating gene 1 - mbp chimera (131 kDa, Protein from Danio rerio)
- Reverse strand of 12-rss substrate dna (15 kDa, DNA from Danio rerio)
- Zinc ion (65 Da, Ligand)
- Recombination activating gene 2 (59 kDa, Protein from Danio rerio)
- Calcium ion (40 Da, Ligand)
- Forward strand of 12-rss substrate dna (15 kDa, DNA from Danio rerio)