Cryo-EM structure of IMPDH2 bound to IMP and GAD
Resolution: 1.82 Å
EM Method: Single-particle
Fitted PDBs: 9dmu
Q-score: 0.802
Chen YJ, Iyer SV, Hsieh DC, Li B, Elias HK, Wang T, Li J, Ganbold M, Lien MC, Peng YC, Xie XP, Jayewickreme CD, van den Brink MRM, Brady SF, Lim SK, Parada LF
Nature (2024) 636 pp. 466-473 [ DOI: doi:10.1038/s41586-024-08224-z Pubmed: 39567689 ]
- Potassium ion (39 Da, Ligand)
- [[(2~{r},3~{s},4~{r},5~{r})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{r},3~{s},4~{r},5~{r})-3,4-bis(oxidanyl)-5-[3-(thiophen-2-ylcarbonylamino)pyridin-1-yl]oxolan-2-yl]methyl hydrogen phosphate (746 Da, Ligand)
- Inosinic acid (348 Da, Ligand)
- Inosine-5'-monophosphate dehydrogenase 2 (56 kDa, Protein from Homo sapiens)
- Ternary complex of impdh2 bound to imp and gad (Complex from Homo sapiens)
- Water (18 Da, Ligand)
Resolution: 1.67 Å
EM Method: Single-particle
Fitted PDBs: 7uur
Q-score: 0.837
Grinter R, Kropp A, Venugopal H, Senger M, Badley J, Cabotaje PR, Jia R, Duan Z, Huang P, Stripp ST, Barlow CK, Belousoff M, Shafaat HS, Cook GM, Schittenhelm RB, Vincent KA, Khalid S, Berggren G, Greening C
Nature (2023) 615 pp. 541-547 [ Pubmed: 36890228 DOI: doi:10.1038/s41586-023-05781-7 ]
- Hydrogenase-2, large subunit (57 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Fe3-s4 cluster (295 Da, Ligand)
- Hydrogenase-2, small subunit (35 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Carbonmonoxide-(dicyano) iron (135 Da, Ligand)
- Nickel (iii) ion (58 Da, Ligand)
- Hydroxide ion (17 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Complex of the type 2 [nife]-hydrogenase huc from mycobacterium smegmatis (833 kDa, Complex from Mycolicibacterium smegmatis)
- Menadione (172 Da, Ligand)
- Water (18 Da, Ligand)
Resolution: 1.52 Å
EM Method: Single-particle
Fitted PDBs: 8dqv
Q-score: 0.857
Grinter R, Kropp A, Venugopal H, Senger M, Badley J, Cabotaje PR, Jia R, Duan Z, Huang P, Stripp ST, Barlow CK, Belousoff M, Shafaat HS, Cook GM, Schittenhelm RB, Vincent KA, Khalid S, Berggren G, Greening C
Nature (2023) 615 pp. 541-547 [ Pubmed: 36890228 DOI: doi:10.1038/s41586-023-05781-7 ]
- Fe3-s4 cluster (295 Da, Ligand)
- Carbonmonoxide-(dicyano) iron (135 Da, Ligand)
- Nickel (iii) ion (58 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Complex of the type 2 [nife]-hydrogenase huc from mycobacterium smegmatis (833 kDa, Complex from Mycolicibacterium smegmatis)
- Menadione (172 Da, Ligand)
- Hydrogenase-2, small subunit (35 kDa, Protein from Mycolicibacterium smegmatis)
- Oxygen atom (15 Da, Ligand)
- Hydrogenase-2, large subunit (57 kDa, Protein from Mycolicibacterium smegmatis)
- Water (18 Da, Ligand)
Translating 70S ribosome in the unrotated state (P and E, tRNAs)
Resolution: 1.55 Å
EM Method: Single-particle
Fitted PDBs: 8b0x
Q-score: 0.767
Fromm SA, O'Connor KM, Purdy M, Bhatt PR, Loughran G, Atkins JF, Jomaa A, Mattei S
Nat Commun (2023) 14 pp. 1095-1095 [ DOI: doi:10.1038/s41467-023-36742-3 Pubmed: 36841832 ]
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli B)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli B)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli B)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli B)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli B)
- P-site trna (24 kDa, RNA from Escherichia coli B)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli B)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli B)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli B)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli B)
- 5s rrna (38 kDa, RNA from Escherichia coli B)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli B)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli B)
- Potassium ion (39 Da, Ligand)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli B)
- 70s ribosome (2 MDa, Complex from Escherichia coli B)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli B)
- 23s rrna (948 kDa, RNA from Escherichia coli B)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli B)
- Water (18 Da, Ligand)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli B)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli B)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli B)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli B)
- 16s rrna (503 kDa, RNA from Escherichia coli B)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli B)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli B)
- Magnesium ion (24 Da, Ligand)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli B)
- Zinc ion (65 Da, Ligand)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli B)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli B)
- Mrna (1 kDa, RNA from Escherichia coli B)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli B)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli B)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli B)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli B)
hBest2 1uM Ca2+ (Ca2+-bound) closed state
Resolution: 1.78 Å
EM Method: Single-particle
Fitted PDBs: 8d1e
Q-score: 0.789
Owji AP, Wang J, Kittredge A, Clark Z, Zhang Y, Hendrickson WA, Yang T
Nat Commun (2022) 13 pp. 3836-3836 [ Pubmed: 35789156 DOI: doi:10.1038/s41467-022-31437-7 ]
- Water (18 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Bestrophin-2 (46 kDa, Protein from Homo sapiens)
- 1,2-dimyristoyl-rac-glycero-3-phosphocholine (677 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- Hbest2 1um ca2+ (ca2+-bound) closed state (234 kDa, Complex from Homo sapiens)
- 2-[2-[(1~{s},2~{s},4~{s},5'~{r},6~{r},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol (516 Da, Ligand)
hBest2 5mM Ca2+ (Ca2+-bound) closed state
Resolution: 1.82 Å
EM Method: Single-particle
Fitted PDBs: 8d1f
Q-score: 0.787
Owji AP, Wang J, Kittredge A, Clark Z, Zhang Y, Hendrickson WA, Yang T
Nat Commun (2022) 13 pp. 3836-3836 [ Pubmed: 35789156 DOI: doi:10.1038/s41467-022-31437-7 ]
- Hbest2 5mm ca2+ (ca2+-bound) closed state (234 kDa, Complex from Homo sapiens)
- Water (18 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Bestrophin-2 (46 kDa, Protein from Homo sapiens)
- 1,2-dimyristoyl-rac-glycero-3-phosphocholine (677 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- 2-[2-[(1~{s},2~{s},4~{s},5'~{r},6~{r},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol (516 Da, Ligand)
hBest2 Ca2+-unbound closed state
Resolution: 1.94 Å
EM Method: Single-particle
Fitted PDBs: 8d1h
Q-score: 0.78
Owji AP, Wang J, Kittredge A, Clark Z, Zhang Y, Hendrickson WA, Yang T
Nat Commun (2022) 13 pp. 3836-3836 [ Pubmed: 35789156 DOI: doi:10.1038/s41467-022-31437-7 ]
- Water (18 Da, Ligand)
- Hbest2 ca2+-unbound closed state (234 kDa, Complex from Homo sapiens)
- Bestrophin-2 (46 kDa, Protein from Homo sapiens)
- 1,2-dimyristoyl-rac-glycero-3-phosphocholine (677 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- 2-[2-[(1~{s},2~{s},4~{s},5'~{r},6~{r},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol (516 Da, Ligand)
bBest2_345 Ca2+-bound open state
Resolution: 1.93 Å
EM Method: Single-particle
Fitted PDBs: 8d1n
Q-score: 0.792
Owji AP, Wang J, Kittredge A, Clark Z, Zhang Y, Hendrickson WA, Yang T
Nat Commun (2022) 13 pp. 3836-3836 [ Pubmed: 35789156 DOI: doi:10.1038/s41467-022-31437-7 ]
- Water (18 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Bbest2_345 ca2+-bound open state (210 kDa, Complex from Bos taurus)
- Bestrophin (40 kDa, Protein from Bos taurus)
- 1,2-dimyristoyl-rac-glycero-3-phosphocholine (677 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- 2-[2-[(1~{s},2~{s},4~{s},5'~{r},6~{r},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol (516 Da, Ligand)