Septin Tetrameric Complex SEPT7/SEPT9 of Ciona intestinalis by Cryo-EM
Resolution: 2.72 Å
EM Method: Single-particle
Fitted PDBs: 9bhw
Q-score: 0.538
Mendonca DC, Morais STB, Ciol H, Pinto APA, Leonardo DA, Pereira HD, Valadares NF, Portugal RV, Klaholz BP, Garratt RC, Araujo APU
J Mol Biol (2024) 436 pp. 168693-168693 [ Pubmed: 38960133 DOI: doi:10.1016/j.jmb.2024.168693 ]
- Ciona intestinalis septin tetrameric complex sept7/sept9 (Complex from Ciona intestinalis)
- Neuronal-specific septin-3 (41 kDa, Protein from Ciona intestinalis)
- Ciseptin-7 (48 kDa, Protein from Ciona intestinalis)
- Guanosine-5'-diphosphate (443 Da, Ligand)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7qhm
Q-score: 0.567
Kao WC, Ortmann de Percin Northumberland C, Cheng TC, Ortiz J, Durand A, von Loeffelholz O, Schilling O, Biniossek ML, Klaholz BP, Hunte C
Nat Commun (2022) 13 pp. 545-545 [ Pubmed: 35087070 DOI: doi:10.1038/s41467-022-28179-x ]
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Hypothetical membrane protein (6 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Manganese (ii) ion (54 Da, Ligand)
- Diacyl glycerol (625 Da, Ligand)
- Lycopene (536 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- (2r)-2-(hexadecanoyloxy)-3-{[(s)-hydroxy{[(1r,2r,3r,4r,5r,6s)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9s)-9-methyloctadecanoate (853 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Thiamine biosynthesis protein x (17 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Palmitic acid (256 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Heme c (618 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Water (18 Da, Ligand)
- Dinuclear copper ion (127 Da, Ligand)
- Hypothetical membrane protein (12 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- [(2~{r})-3-[[(1~{s},2~{r},3~{s},4~{s},5~{r},6~{r})-2-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-[[(2~{s},3~{s},4~{s},5~{s},6~{r})-6-[[(2~{s},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{r},3~{s},4~{s},5~{s},6~{r})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{r})-10-methyldodecanoate (1 kDa, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Uncharacterized protein cgl2664/cg2949 (16 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Heme-as (920 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome c oxidase subunit 2 (36 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Uncharacterized membrane protein cgl2017/cg2211 (16 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Stigmatellin a (514 Da, Ligand)
- [(2~{r})-3-[[(1~{s},2~{r},3~{r},4~{s},5~{s},6~{r})-2-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{s})-10-methylhenicosanoate (1 kDa, Ligand)
- Calcium ion (40 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Oxygen molecule (31 Da, Ligand)
- Actinobacterial supercomplex, subunit c (ascc) (8 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome bcc-aa3 supercomplex (Complex from Corynebacterium glutamicum ATCC 13032)
- Cytochrome bc1 complex rieske iron-sulfur subunit (45 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome c oxidase subunit 1 (66 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Menaquinone-9 (785 Da, Ligand)
- Azide ion (42 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
High-resolution cryo-EM structure of the human 80S ribosome - (composite structure)
Natchiar SK, Myasnikov AG, Kratzat H, Hazemann I, Klaholz BP
Nature (2017) 551 pp. 472-477 [ DOI: doi:10.1038/nature24482 Pubmed: 29143818 ]
- 60s ribosomal protein l38 (8 kDa, Protein from Human)
- 60s ribosomal protein l29 (17 kDa, Protein from Human)
- 40s ribosomal protein s6 (28 kDa, Protein from Human)
- 60s ribosomal protein l23a (17 kDa, Protein from Human)
- 60s ribosomal protein l24 (17 kDa, Protein from Human)
- 5.8s ribosomal rna (50 kDa, RNA from Human)
- 60s ribosomal protein l41 (3 kDa, Protein from Human)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Human)
- 60s ribosomal protein l14 (23 kDa, Protein from Human)
- 60s ribosomal protein l17 (21 kDa, Protein from Human)
- 60s ribosomal protein l4 (47 kDa, Protein from Human)
- 60s ribosomal protein l39 (6 kDa, Protein from Human)
- 60s ribosomal protein l15 (24 kDa, Protein from Human)
- 40s ribosomal protein s15 (17 kDa, Protein from Human)
- 40s ribosomal protein s16 (16 kDa, Protein from Human)
- 60s ribosomal protein l9 (21 kDa, Protein from Human)
- 40s ribosomal protein s19 (16 kDa, Protein from Human)
- 60s ribosomal protein l6 (32 kDa, Protein from Human)
- 5s ribosomal rna (38 kDa, RNA from Human)
- 60s ribosomal protein l26 (17 kDa, Protein from Human)
- 60s ribosomal protein l30 (12 kDa, Protein from Human)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Human)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Human)
- 60s ribosomal protein l27 (15 kDa, Protein from Human)
- 60s ribosomal protein l7 (29 kDa, Protein from Human)
- 80s ribosome with ligand hht and hyg (4 MDa, Complex from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Human)
- 60s ribosomal protein l21 (18 kDa, Protein from Human)
- 40s ribosomal protein s11 (18 kDa, Protein from Human)
- 40s ribosomal protein s18 (17 kDa, Protein from Human)
- 60s ribosomal protein l28 (15 kDa, Protein from Human)
- 40s ribosomal protein s13 (17 kDa, Protein from Human)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s27 (9 kDa, Protein from Human)
- 60s ribosomal protein l19 (23 kDa, Protein from Human)
- 40s ribosomal protein s23 (15 kDa, Protein from Human)
- 40s ribosomal protein s10 (18 kDa, Protein from Human)
- 40s ribosomal protein s5 (22 kDa, Protein from Human)
- 18s ribosomal rna (603 kDa, RNA from Human)
- 60s ribosomal protein l13 (24 kDa, Protein from Human)
- 40s ribosomal protein s25 (13 kDa, Protein from Human)
- 60s ribosomal protein l32 (15 kDa, Protein from Human)
- 60s ribosomal protein l22 (14 kDa, Protein from Human)
- 60s ribosomal protein l27a (16 kDa, Protein from Human)
- 40s ribosomal protein s20 (13 kDa, Protein from Human)
- 28s ribosomal rna (1 MDa, RNA from Human)
- 60s ribosomal protein l31 (14 kDa, Protein from Human)
- 60s ribosomal protein l5 (34 kDa, Protein from Human)
- 40s ribosomal protein s24 (15 kDa, Protein from Human)
- 40s ribosomal protein s15a (14 kDa, Protein from Human)
- 60s ribosomal protein l37a (10 kDa, Protein from Human)
- 60s ribosomal protein l11 (20 kDa, Protein from Human)
- (3beta)-o~3~-[(2r)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine (545 Da, Ligand)
- 40s ribosomal protein s29 (6 kDa, Protein from Human)
- 60s ribosomal protein l10-like (24 kDa, Protein from Human)
- 40s ribosomal protein s3 (26 kDa, Protein from Human)
- 60s ribosomal protein l8 (28 kDa, Protein from Human)
- 60s ribosomal protein l10a (24 kDa, Protein from Human)
- 60s ribosomal protein l36a (12 kDa, Protein from Human)
- 40s ribosomal protein sa (32 kDa, Protein from Human)
- 60s ribosomal protein l23 (14 kDa, Protein from Human)
- 40s ribosomal protein s12 (14 kDa, Protein from Human)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l36 (12 kDa, Protein from Human)
- 40s ribosomal protein s17 (15 kDa, Protein from Human)
- 60s ribosomal protein l13a (23 kDa, Protein from Human)
- 60s ribosomal protein l35a (12 kDa, Protein from Human)
- 40s ribosomal protein s30 (6 kDa, Protein from Human)
- 60s ribosomal protein l35 (14 kDa, Protein from Human)
- Water (18 Da, Ligand)
- 60s ribosomal protein l3 (46 kDa, Protein from Human)
- 40s ribosomal protein s3a (30 kDa, Protein from Human)
- 60s ribosomal protein l18 (21 kDa, Protein from Human)
- 60s ribosomal protein l18a (20 kDa, Protein from Human)
- 40s ribosomal protein s2 (31 kDa, Protein from Human)
- 60s ribosomal protein l37 (11 kDa, Protein from Human)
- 40s ribosomal protein s14 (16 kDa, Protein from Human)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Human)
- 40s ribosomal protein s28 (7 kDa, Protein from Human)
- 40s ribosomal protein s7 (22 kDa, Protein from Human)
- Human initiator met-trna-i (24 kDa, RNA from Human)
- 60s ribosomal protein l7a (30 kDa, Protein from Human)
- 40s ribosomal protein s21 (9 kDa, Protein from Human)
- 60s ribosomal protein l34 (13 kDa, Protein from Human)
- Hygromycin b (527 Da, Ligand)
- 40s ribosomal protein s9 (22 kDa, Protein from Human)
- 40s ribosomal protein s8 (24 kDa, Protein from Human)