Cryo-EM structure of the PSI-LHCI-Lhcp supercomplex from Ostreococcus tauri
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 7yca
Q-score: 0.514
Ishii A, Shan J, Sheng X, Kim E, Watanabe A, Yokono M, Noda C, Song C, Murata K, Liu Z, Minagawa J
eLife (2023) 12 [ Pubmed: 36951548 DOI: doi:10.7554/eLife.84488 ]
- Psag (14 kDa, Protein from Ostreococcus tauri)
- Phylloquinone (450 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (26 kDa, Protein from Ostreococcus tauri)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Ostreococcus tauri)
- Chlorophyll a-b binding protein, chloroplastic (29 kDa, Protein from Ostreococcus tauri)
- Beta-carotene (536 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (25 kDa, Protein from Ostreococcus tauri)
- Photosystem i psan, reaction centre subunit n (14 kDa, Protein from Ostreococcus tauri)
- Photosystem i psah, reaction centre subunit vi (17 kDa, Protein from Ostreococcus tauri)
- Psi subunit v (21 kDa, Protein from Ostreococcus tauri)
- (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol (600 Da, Ligand)
- Lhca6 (26 kDa, Protein from Ostreococcus tauri)
- Photosystem i reaction center subunit ii, chloroplastic (20 kDa, Protein from Ostreococcus tauri)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Ostreococcus tauri)
- Chlorophyll b (907 Da, Ligand)
- Chlorophyll c2 (608 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Ostreococcus tauri)
- Water (18 Da, Ligand)
- Photosystem i-light-harvesting complex i-prasinophyte-specific lhc protein (psi-lhci-lhcp) supercomplex (Complex from Ostreococcus tauri)
- Psao (15 kDa, Protein from Ostreococcus tauri)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Ostreococcus tauri)
- (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)
- Photosystem i reaction center subunit iii (24 kDa, Protein from Ostreococcus tauri)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction centre subunit iv (11 kDa, Protein from Ostreococcus tauri)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Ostreococcus tauri)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Ostreococcus tauri)
- (1~{s})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaenyl]cyclohex-3-en-1-ol (570 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Ostreococcus tauri)
- (3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-1-[(1~{s},4~{s})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one (600 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Ostreococcus tauri)
- Lhca1 (24 kDa, Protein from Ostreococcus tauri)
- Photosystem i iron-sulfur center (8 kDa, Protein from Ostreococcus tauri)
- Photosystem i psag/psak protein (13 kDa, Protein from Ostreococcus tauri)
- Iron/sulfur cluster (351 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
Cryo-EM structure of the Lhcp complex from Ostreococcus tauri
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 8hg3
Q-score: 0.479
Ishii A, Shan J, Sheng X, Kim E, Watanabe A, Yokono M, Noda C, Song C, Murata K, Liu Z, Minagawa J
eLife (2023) 12 [ Pubmed: 36951548 DOI: doi:10.7554/eLife.84488 ]
- (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol (600 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Ostreococcus tauri)
- Chlorophyll b (907 Da, Ligand)
- Chlorophyll c2 (608 Da, Ligand)
- Prasinophyte-specific lhc protein (lhcp) complex (Complex from Ostreococcus tauri)
- Chlorophyll a (893 Da, Ligand)
- (1~{s})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaenyl]cyclohex-3-en-1-ol (570 Da, Ligand)
- (3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-1-[(1~{s},4~{s})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one (600 Da, Ligand)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8hg5
Q-score: 0.486
Ishii A, Shan J, Sheng X, Kim E, Watanabe A, Yokono M, Noda C, Song C, Murata K, Liu Z, Minagawa J
eLife (2023) 12 [ Pubmed: 36951548 DOI: doi:10.7554/eLife.84488 ]
- (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol (600 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Ostreococcus tauri)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Ostreococcus tauri)
- Cryo-em structure of the prasinophyte-specific light-harvesting complex (lhcp)from ostreococcus tauri (Complex from Ostreococcus tauri)
- Chlorophyll b (907 Da, Ligand)
- Chlorophyll c2 (608 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- (1~{s})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaenyl]cyclohex-3-en-1-ol (570 Da, Ligand)
- (3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-1-[(1~{s},4~{s})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one (600 Da, Ligand)
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 8hg6
Q-score: 0.412
Ishii A, Shan J, Sheng X, Kim E, Watanabe A, Yokono M, Noda C, Song C, Murata K, Liu Z, Minagawa J
eLife (2023) 12 [ Pubmed: 36951548 DOI: doi:10.7554/eLife.84488 ]
- (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol (600 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Ostreococcus tauri)
- Chlorophyll b (907 Da, Ligand)
- Chlorophyll c2 (608 Da, Ligand)
- Prasinophyte-specific lhc protein (lhcp) complex (Complex from Ostreococcus tauri)
- Chlorophyll a (893 Da, Ligand)
- (1~{s})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaenyl]cyclohex-3-en-1-ol (570 Da, Ligand)
- (3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-1-[(1~{s},4~{s})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one (600 Da, Ligand)
Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the arylsulfonamide inhibitor GNE-3565
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8f0r
Q-score: 0.556
Kschonsak M, Jao CC, Arthur CP, Rohou AL, Bergeron P, Ortwine DF, McKerrall SJ, Hackos DH, Deng L, Chen J, Li T, Dragovich PS, Volgraf M, Wright MR, Payandeh J, Ciferri C, Tellis JC
eLife (2023) 12 [ Pubmed: 36975198 DOI: doi:10.7554/eLife.84151 ]
- Sodium channel protein pafpc1,sodium channel protein type 9 subunit alpha chimera (184 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Vsd4-nav1.7-navpas channel chimera bound to the arylsulfonamide inhibitor gne-3565 (Complex from Homo sapiens)
- Cholesterol hemisuccinate (486 Da, Ligand)
- 5-chloro-4-({(1s,2s,4s)-2-(dimethylamino)-4-[3-(trifluoromethyl)phenyl]cyclohexyl}amino)-2-fluoro-n-(pyrimidin-4-yl)benzene-1-sulfonamide (572 Da, Ligand)
ARE-ABCF VmlR2 bound to a 70S ribosome
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8buu
Q-score: 0.514
Obana N, Takada H, Crowe-McAuliffe C, Iwamoto M, Egorov AA, Wu KJY, Chiba S, Murina V, Paternoga H, Tresco BIC, Nomura N, Myers AG, Atkinson GC, Wilson DN, Hauryliuk V
Nucleic Acids Res (2023) 51 pp. 4536-4554 [ Pubmed: 36951104 DOI: doi:10.1093/nar/gkad193 ]
- 30s ribosomal protein s2 (28 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 16s rrna (503 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l15 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 5s rrna (38 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l17 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Expz (72 kDa, Protein from Neobacillus vireti)
- 50s ribosomal protein l33 1 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l13 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l24 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l30 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l21 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l6 (19 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Potassium ion (39 Da, Ligand)
- 50s ribosomal protein l20 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l35 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l28 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s17 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 50s ribosomal protein l36 (4 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s19 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l3 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l19 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l22 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l5 (20 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l14 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Trna-fmet (24 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l2 (30 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Mrna (4 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Magnesium ion (24 Da, Ligand)
- 30s ribosomal protein s16 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l23 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s14 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 23s rrna (949 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l27 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s11 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Zinc ion (65 Da, Ligand)
- 70s ribosome with vmlr2 bound in the e site, a distorted trna in the p site, and a substoichiometric distorted trna in the a site (2 MDa, Complex from Neobacillus vireti)
- 50s ribosomal protein l16 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l18 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l34 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l29 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s9 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s10 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s3 (24 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s13 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l32 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
SIRT6 bound to an H3K9Ac nucleosome
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8f86
Q-score: 0.434
Wang ZA, Markert JW, Whedon SD, Yapa Abeywardana M, Lee K, Jiang H, Suarez C, Lin H, Farnung L, Cole PA
J Am Chem Soc (2023) 145 pp. 6811-6822 [ DOI: doi:10.1021/jacs.2c13512 Pubmed: 36930461 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- [(2r,3s,4r,5r)-5-(6-amino-9h-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3ar,5r,6r,6ar)-6-hydroxytetrahydro-2h-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name) (587 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Sirt6 bound to h3k9ac (Complex)
- Dna (148-mer) (56 kDa, DNA from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Nad-dependent protein deacylase sirtuin-6 (39 kDa, Protein from Homo sapiens)
- Dna (148-mer) (57 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Resolution: 2.02 Å
EM Method: Single-particle
Fitted PDBs: 8g6w
Q-score: 0.628
Majumdar C, Walker JA, Francis MB, Schepartz A, Cate JHD
ACS Cent Sci (2023) 9 pp. 1160-1169 [ DOI: doi:10.1021/acscentsci.3c00153 Pubmed: 37396857 ]
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 23s rrna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- P-site fmet-trnafmet (24 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) (346 Da, Ligand)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- Paromomycin (615 Da, Ligand)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
- Potassium ion (39 Da, Ligand)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- A-site oabz-trnaphe (24 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 2-amino-benzamide (136 Da, Ligand)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- Spermidine (145 Da, Ligand)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- N-formylmethionine (177 Da, Ligand)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 70s e.coli ribosome (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- Mrna (9 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- 16s rrna (499 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- Ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
High resolution cry-EM structure of the human 80S ribosome from SNORD127+/+ Kasumi-1 cells
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7xnx
Q-score: 0.58
Zhou F, Aroua N, Liu Y, Rohde C, Cheng J, Wirth AK, Fijalkowska D, Gollner S, Lotze M, Yun H, Yu X, Pabst C, Sauer T, Oellerich T, Serve H, Rollig C, Bornhauser M, Thiede C, Baldus C, Frye M, Raffel S, Krijgsveld J, Jeremias I, Beckmann R, Trumpp A, Muller-Tidow C
Cancer Discov (2023) 13 pp. 332-347 [ Pubmed: 36259929 DOI: doi:10.1158/2159-8290.CD-22-0210 ]
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- 5s rrna (38 kDa, RNA from Homo sapiens)
- 60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
- Ribosome (Complex from Homo sapiens)
- 18s rrna (603 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- 28s rrna (1 MDa, RNA from Homo sapiens)
- 60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l7 (29 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l27 (32 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l8 (28 kDa, Protein from Homo sapiens)
- Trna (24 kDa, RNA from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- Ribosomal protein l10 isoform a (24 kDa, Protein from Homo sapiens)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- 5.8s rrna (50 kDa, RNA from Homo sapiens)
- 60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
High resolution cry-EM structure of the human 80S ribosome from SNORD127+/- Kasumi-1 cells
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7xny
Q-score: 0.56
Zhou F, Aroua N, Liu Y, Rohde C, Cheng J, Wirth AK, Fijalkowska D, Gollner S, Lotze M, Yun H, Yu X, Pabst C, Sauer T, Oellerich T, Serve H, Rollig C, Bornhauser M, Thiede C, Baldus C, Frye M, Raffel S, Krijgsveld J, Jeremias I, Beckmann R, Trumpp A, Muller-Tidow C
Cancer Discov (2023) 13 pp. 332-347 [ Pubmed: 36259929 DOI: doi:10.1158/2159-8290.CD-22-0210 ]
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- 60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
- Ribosome (Complex from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
- 18s rrna (603 kDa, RNA from Homo sapiens)
- 60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- 28s rrna (1 MDa, RNA from Homo sapiens)
- 60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l27a (16 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l7 (29 kDa, Protein from Homo sapiens)
- 5s rrna (38 kDa, RNA from Homo sapiens)
- 5.8s rrna (50 kDa, RNA from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l8 (28 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- Ribosomal protein l10 isoform a (24 kDa, Protein from Homo sapiens)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)