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The electron crystallography structure of the cAMP-bound potassium channel MloK1 (PCO-refined)
Resolution: 4.5 Å
EM Method: Electron Crystallography
Fitted PDBs: 6eo1
Q-score: 0.184
Kowal J, Biyani N, Chami M, Scherer S, Rzepiela AJ, Baumgartner P, Upadhyay V, Nimigean CM, Stahlberg H
Structure (2018) 26 pp. 20-27.e3 [ Pubmed: 29249605 DOI: doi:10.1016/j.str.2017.11.012 ]
- Potassium ion (39 Da, Ligand)
- Mlok1 tetramer (148 kDa, Complex from Mesorhizobium loti)
- Cyclic nucleotide-gated potassium channel mll3241 (37 kDa, Protein from Mesorhizobium loti MAFF303099)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 5t62
Q-score: 0.477
Malyutin AG, Musalgaonkar S, Patchett S, Frank J, Johnson AW
EMBO J (2017) 36 pp. 854-868 [ DOI: doi:10.15252/embj.201696012 Pubmed: 28179369 ]
- 60s ribosomal protein l30 (11 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l8-a (28 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l31-a (12 kDa, Protein from Baker's yeast)
- 5s ribosomal rna (38 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l25 (15 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l26-a (14 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l14-a (15 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l23-a (14 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l17-a (20 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l4-a (39 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l15-a (24 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l38 (8 kDa, Protein from Baker's yeast)
- Large subunit gtpase 1 (71 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l32 (14 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l37-a (9 kDa, Protein from Baker's yeast)
- Eukaryotic translation initiation factor 6 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l11-a (19 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l35-a (13 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l18-a (20 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l9-a (21 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l39 (6 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l28 (16 kDa, Protein from Baker's yeast)
- 60s in complex with nmd3, lsg1, and tif6 (Complex from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l2-a (27 kDa, Protein from Baker's yeast)
- Potassium ion (39 Da, Ligand)
- 60s ribosomal protein l3 (43 kDa, Protein from Baker's yeast)
- 25s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae S288c)
- 60s ribosomal protein l19-a (21 kDa, Protein from Baker's yeast)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- 60s ribosomal protein l10 (25 kDa, Protein from Baker's yeast)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Baker's yeast)
- 60s-nmd3-tif6-lsg1 complex with focus on nmd3 (Complex from Saccharomyces cerevisiae)
- 60s ribosomal protein l7-a (27 kDa, Protein from Baker's yeast)
- 5.8s ribosomal rna (50 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l29 (6 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l33-a (12 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l5 (33 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l42-a (12 kDa, Protein from Baker's yeast)
- Ribosomal protein ul1 (18 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l34-a (13 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l6-a (20 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l27-a (15 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l16-a (22 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l20-a (20 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l24-a (17 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l36-a (11 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l43-a (10 kDa, Protein from Baker's yeast)
- Water (18 Da, Ligand)
- 60s ribosomal protein l13-a (22 kDa, Protein from Baker's yeast)
- 60s ribosomal export protein nmd3 (59 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l22-a (13 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l21-a (18 kDa, Protein from Baker's yeast)
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 5t6r
Q-score: 0.325
Malyutin AG, Musalgaonkar S, Patchett S, Frank J, Johnson AW
EMBO J (2017) 36 pp. 854-868 [ DOI: doi:10.15252/embj.201696012 Pubmed: 28179369 ]
- 60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 5s ribosomal rna (38 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l39 (6 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s in complex with nmd3 (Complex from Saccharomyces cerevisiae)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Potassium ion (39 Da, Ligand)
- Maltose binding protein, 60s ribosomal export protein nmd3 fusion (103 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 25s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ribosomal protein ul1 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 5.8s ribosomal rna (50 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l11-a (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Water (18 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of a spliceosome remodeled for exon ligation
Resolution: 3.85 Å
EM Method: Single-particle
Fitted PDBs: 5mps
Q-score: 0.356
Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ, Nagai K
Nature (2017) 542 pp. 377-380 [ DOI: doi:10.1038/nature21078 Pubmed: 28076345 ]
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Baker's yeast)
- Zinc ion (65 Da, Ligand)
- Inositol hexakisphosphate (660 Da, Ligand)
- Pre-mrna-splicing factor cef1 (67 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Baker's yeast)
- Ubc4 gene exon (6 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 18 (28 kDa, Protein from Baker's yeast)
- Potassium ion (39 Da, Ligand)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor slu7 (44 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor syf1 (101 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor clf1 (82 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Baker's yeast)
- Saccharomyces cerevisiae strain t.52_2h chromosome xii sequence (35 kDa, RNA from Saccharomyces cerevisiae)
- Saccharomyces cerevisiae spliceosome. complex c just after prp16-mediated remodeling (Complex)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Baker's yeast)
- Pre-mrna-processing factor 17 (52 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Baker's yeast)
- Unknown (5 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Baker's yeast)
- U5 snrna (57 kDa, RNA from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Baker's yeast)
- U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Baker's yeast)
- Magnesium ion (24 Da, Ligand)
- Yeast ubc4 gene for ubiquitin-conjugating enzyme (30 kDa, RNA from Saccharomyces cerevisiae)
Structure of a spliceosome remodeled for exon ligation
Resolution: 4.17 Å
EM Method: Single-particle
Fitted PDBs: 5mq0
Q-score: 0.223
Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ, Nagai K
Nature (2017) 542 pp. 377-380 [ DOI: doi:10.1038/nature21078 Pubmed: 28076345 ]
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Baker's yeast)
- Saccharomyces cerevisiae strain wi_c_mbsp_4 chromosome vii sequence (57 kDa, RNA from Baker's yeast)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Baker's yeast)
- Zinc ion (65 Da, Ligand)
- Inositol hexakisphosphate (660 Da, Ligand)
- Pre-mrna-splicing factor cef1 (67 kDa, Protein from Baker's yeast)
- Saccharomyces cerevisiae strain t.52_2h chromosome xii sequence (35 kDa, RNA from Baker's yeast)
- Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor atp-dependent rna helicase prp22 (130 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Baker's yeast)
- S.cerevisiae chromosome ii reading frame orf ybr230c (376 kDa, RNA from Baker's yeast)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Baker's yeast)
- Potassium ion (39 Da, Ligand)
- Pre-mrna-splicing factor 18 (28 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Baker's yeast)
- U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor snt309 (20 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor slu7 (44 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor clf1 (82 kDa, Protein from Baker's yeast)
- U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Baker's yeast)
- Saccharomyces cerevisiae spliceosome. complex c just after prp16-mediated remodeling (Complex)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Baker's yeast)
- 5'-exon of ubc4 pre-mrna (6 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Baker's yeast)
- Pre-mrna-processing factor 17 (52 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Baker's yeast)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor syf1,pre-mrna-splicing factor syf1 (101 kDa, Protein from Baker's yeast)
- Pre-mrna-processing factor 19 (56 kDa, Protein from Baker's yeast)
- 3'-exon of ubc4 pre-mrna, bound by prp22 helicase (873 Da, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Baker's yeast)
- Magnesium ion (24 Da, Ligand)
- Unknown protein (5 kDa, Protein from Baker's yeast)
- Yeast ubc4 gene for ubiquitin-conjugating enzyme (30 kDa, RNA from Saccharomyces cerevisiae)
Structure of a spliceosome remodeled for exon ligation
Fica SM, Galej WP, Wilkinson ME, Oubridge C, Bai X-C, Newman AJ, Nagai K
Nature (2017) 542 pp. 377-380 [ DOI: doi:10.1038/nature21078 Pubmed: 28076345 ]
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Baker's yeast)
- U6 snrna (35 kDa, RNA from Baker's yeast)
- 3'exon of ubc4 pre-mrna bound to prp22 helicase (873 Da, RNA from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Inositol hexakisphosphate (660 Da, Ligand)
- Pre-mrna-splicing factor cef1 (67 kDa, Protein from Baker's yeast)
- Pre-mrna-processing factor 17 (52 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor atp-dependent rna helicase prp22 (130 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Baker's yeast)
- Intron of ubc4 pre-mrna (30 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Baker's yeast)
- Potassium ion (39 Da, Ligand)
- Pre-mrna-splicing factor 18 (28 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Baker's yeast)
- U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor slu7 (44 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor clf1 (82 kDa, Protein from Baker's yeast)
- 5'exon of ubc4 pre-mrna (6 kDa, RNA from Saccharomyces cerevisiae)
- U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Baker's yeast)
- Saccharomyces cerevisiae spliceosome. complex c just after prp16-mediated remodeling (Complex)
- U5 snrna (57 kDa, RNA from Baker's yeast)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Baker's yeast)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Baker's yeast)
- Magnesium ion (24 Da, Ligand)
- Unknown protein (5 kDa, Protein from Baker's yeast)
- U2 snrna (376 kDa, RNA from Baker's yeast)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 5tj6
Q-score: 0.4
Nature (2017) 541 pp. 46-51 [ Pubmed: 27974795 DOI: doi:10.1038/nature20608 ]
- High conductance calcium-activated potassium channel (120 kDa, Protein from Aplysia californica)
- Calcium ion (40 Da, Ligand)
- Ca2+ bound aplysia slo1 (400 kDa, Cellular component from Aplysia californica)
- (1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
- Potassium ion (39 Da, Ligand)
- Magnesium ion (24 Da, Ligand)