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sample_name:"Pre-mRNA-splicing factor SYF1" AND xref_links:"pdb" AND author_name:"Nagai"

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EMD-4525

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Human post-catalytic spliceosome (P complex) stalled with DHX8 K594A mutant, overall map

Release date: Feb. 20, 2019
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6qdv
Q-score: 0.278

Fica SM, Oubridge C, Wilkinson ME, Newman AJ, Nagai K

Science (2019) 363 pp. 710-714 [ DOI: doi:10.1126/science.aaw5569 Pubmed: 30705154 ]

Sample:

Human post-catalytic p complex spliceosome (3 MDa, Complex)
Intron lariat: minx rna (27 kDa, RNA from Human adenovirus 2)
U2 small nuclear ribonucleoprotein b'' (10 kDa, Protein from Homo sapiens)
Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from Homo sapiens)
Human post-catalytic p complex spliceosome (Complex from Homo sapiens)
116 kda u5 small nuclear ribonucleoprotein component (101 kDa, Protein from Homo sapiens)
Protein fam32a (7 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein sm d1 (9 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
Peptidyl-prolyl cis-trans isomerase-like 1 (18 kDa, Protein from Homo sapiens)
Crooked neck-like protein 1 (100 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein f (8 kDa, Protein from Homo sapiens)
Serine/arginine repetitive matrix protein 2 (2 kDa, Protein from Homo sapiens)
Pre-mrna-splicing factor cwc22 homolog (105 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein sm d3 (9 kDa, Protein from Homo sapiens)
Cactin (15 kDa, Protein from Homo sapiens)
U6 snrna (34 kDa, RNA from Homo sapiens)
Potassium ion (39 Da, Ligand)
U2 snrna (60 kDa, RNA from Homo sapiens)
Guanosine-5'-triphosphate (523 Da, Ligand)
Atp-dependent rna helicase dhx8 (139 kDa, Protein from Homo sapiens)
Adenosine-5'-triphosphate (507 Da, Ligand)
Prkr-interacting protein 1 (14 kDa, Protein from Homo sapiens)
Protein bud31 homolog (17 kDa, Protein from Homo sapiens)
U5 snrna (36 kDa, RNA from Homo sapiens)
U5 small nuclear ribonucleoprotein 200 kda helicase (197 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein e (9 kDa, Protein from Homo sapiens)
Pre-mrna-splicing factor rbm22 (33 kDa, Protein from Homo sapiens)
Eukaryotic initiation factor 4a-iii, n-terminally processed (44 kDa, Protein from Homo sapiens)
U5 small nuclear ribonucleoprotein 40 kda protein (34 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
Pre-mrna-splicing factor syf2 (17 kDa, Protein from Homo sapiens)
Snw domain-containing protein 1 (33 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein-associated proteins b and b' (9 kDa, Protein from Homo sapiens)
Atp-dependent rna helicase dhx8 (Complex from Homo sapiens)
Pre-mrna-processing factor 17 (59 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
Replication stress response regulator sde2 (4 kDa, Protein from Homo sapiens)
Cell division cycle 5-like protein (92 kDa, Protein from Homo sapiens)
Protein mago nashi homolog 2 (16 kDa, Protein from Homo sapiens)
Ligated exons: minx mrna (4 kDa, RNA from Human adenovirus 2)
Pre-mrna-processing factor 19 (55 kDa, Protein from Homo sapiens)
Rna-binding protein 8a (10 kDa, Protein from Homo sapiens)
Intron-binding protein aquarius (171 kDa, Protein from Homo sapiens)
Pre-mrna-splicing factor syf1 (100 kDa, Protein from Homo sapiens)
Pre-mrna-splicing factor slu7 (68 kDa, Protein from Homo sapiens)
Nf-kappa-b-activating protein (3 kDa, Protein from Homo sapiens)
U2 small nuclear ribonucleoprotein a' (18 kDa, Protein from Homo sapiens)
Pleiotropic regulator 1 (35 kDa, Protein from Homo sapiens)
Pre-mrna-splicing factor spf27 (26 kDa, Protein from Homo sapiens)
Minx introns and exons (Complex from Human adenovirus 2)
Inositol hexakisphosphate (660 Da, Ligand)
Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from Homo sapiens)

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EMD-3979

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Post-catalytic P complex spliceosome with 3' splice site docked

Release date: Jan. 17, 2018
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6exn
Q-score: 0.296

Wilkinson ME, Fica SM, Galej WP, Norman CM, Newman AJ, Nagai K

Science (2017) 358 pp. 1283-1288 [ DOI: doi:10.1126/science.aar3729 Pubmed: 29146871 ]

Sample:

Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Baker's yeast)
U6 snrna (35 kDa, RNA from Baker's yeast)
Pre-mrna-splicing factor prp8 (279 kDa, Protein from Baker's yeast)
Small nuclear ribonucleoprotein f (9 kDa, Protein from Baker's yeast)
Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Baker's yeast)
Pre-mrna-splicing factor slt11 (40 kDa, Protein from Baker's yeast)
Pre-mrna-splicing factor cef1 (67 kDa, Protein from Baker's yeast)
Unassigned structure (8 kDa, Protein from Baker's yeast)
Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Baker's yeast)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Baker's yeast)
U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Baker's yeast)
Pre-mrna-splicing factor prp46 (50 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 cwc21 (15 kDa, Protein from Baker's yeast)
U5 snrna (57 kDa, RNA from Baker's yeast)
3' exon (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor snu114 (114 kDa, Protein from Baker's yeast)
Pre-mrna-splicing factor prp18 (28 kDa, Protein from Baker's yeast)
Ligated exons: ubc4 mrna (12 kDa, RNA from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor clf1 (82 kDa, Protein from Baker's yeast)
Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Baker's yeast)
Intron lariat: ubc4 rna (30 kDa, RNA from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor syf1 (100 kDa, Protein from Baker's yeast)
Pre-mrna-splicing factor slu7 (44 kDa, Protein from Baker's yeast)
Magnesium ion (24 Da, Ligand)
U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Baker's yeast)
Pre-mrna-processing factor prp19 (56 kDa, Protein from Baker's yeast)
Zinc ion (65 Da, Ligand)
U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor snt309 (20 kDa, Protein from Baker's yeast)
Inositol hexakisphosphate (660 Da, Ligand)
Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Baker's yeast)
Guanosine-5'-triphosphate (523 Da, Ligand)
Pre-mrna-processing protein 45 (42 kDa, Protein from Baker's yeast)
Pre-mrna-processing factor prp17 (52 kDa, Protein from Baker's yeast)
P complex spliceosome with 3' exon docked (2 MDa, Complex)
Pre-mrna-splicing factor syf2 (24 kDa, Protein from Baker's yeast)
Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Baker's yeast)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Baker's yeast)
P complex spliceosome (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Baker's yeast)
Pre-mrna-splicing factor bud31 (18 kDa, Protein from Baker's yeast)
Pre-mrna-splicing factor cwc16 (32 kDa, Protein from Baker's yeast)

[Show more]

EMD-3539

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Structure of a spliceosome remodeled for exon ligation

Release date: Jan. 18, 2017
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 ]

Sample:

Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
Ubc4 gene exon (6 kDa, RNA from Saccharomyces cerevisiae)
Pre-mrna-splicing factor slu7 (44 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor cef1 (67 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor 18 (28 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Saccharomyces cerevisiae)
Yeast ubc4 gene for ubiquitin-conjugating enzyme (30 kDa, RNA from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae)
Potassium ion (39 Da, Ligand)
Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae)
Guanosine-5'-triphosphate (523 Da, Ligand)
Unknown (5 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor clf1 (82 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae)
U5 snrna (57 kDa, RNA from Saccharomyces cerevisiae)
Pre-mrna-processing factor 17 (52 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
Magnesium ion (24 Da, Ligand)
Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
Inositol hexakisphosphate (660 Da, Ligand)
Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
Zinc ion (65 Da, Ligand)
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-splicing factor syf1 (101 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)

[Show more]

EMD-3541

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Structure of a spliceosome remodeled for exon ligation

Release date: Jan. 18, 2017
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 ]

Sample:

Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor slu7 (44 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor cef1 (67 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor 18 (28 kDa, Protein from Saccharomyces cerevisiae)
Unknown protein (5 kDa, Protein from Saccharomyces cerevisiae)
Saccharomyces cerevisiae strain wi_c_mbsp_4 chromosome vii sequence (57 kDa, RNA from Saccharomyces cerevisiae)
Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Saccharomyces cerevisiae)
Yeast ubc4 gene for ubiquitin-conjugating enzyme (30 kDa, RNA from Saccharomyces cerevisiae)
U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae)
U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
3'-exon of ubc4 pre-mrna, bound by prp22 helicase (873 Da, RNA from Saccharomyces cerevisiae)
Potassium ion (39 Da, Ligand)
Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae)
Guanosine-5'-triphosphate (523 Da, Ligand)
Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor clf1 (82 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor snt309 (20 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-processing factor 19 (56 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-processing factor 17 (52 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor atp-dependent rna helicase prp22 (130 kDa, Protein from Saccharomyces cerevisiae)
Magnesium ion (24 Da, Ligand)
Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
Inositol hexakisphosphate (660 Da, Ligand)
Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
Zinc ion (65 Da, Ligand)
Saccharomyces cerevisiae strain t.52_2h chromosome xii sequence (35 kDa, RNA from Saccharomyces cerevisiae)
Pre-mrna-splicing factor syf1,pre-mrna-splicing factor syf1 (101 kDa, Protein from Saccharomyces cerevisiae)
Saccharomyces cerevisiae spliceosome. complex c just after prp16-mediated remodeling (Complex)
S.cerevisiae chromosome ii reading frame orf ybr230c (376 kDa, RNA from Saccharomyces cerevisiae)
5'-exon of ubc4 pre-mrna (6 kDa, RNA from Saccharomyces cerevisiae)
Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)

[Show more]

EMD-4057

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Structure of the yeast spliceosome immediately after branching. 3D class containing helicase module.

Release date: Aug. 31, 2016
Resolution: 10.0 Å
EM Method: Single-particle
Fitted PDBs: 5lj5
Q-score: 0.114

Galej WP, Wilkinson ME, Fica SM, Oubridge C, Newman AJ, Nagai K

Nature (2016) 537 pp. 197-201 [ DOI: doi:10.1038/nature19316 Pubmed: 27459055 ]

Sample:

Pre-mrna-splicing factor isy1 (28 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor cef1 (67 kDa, Protein from Saccharomyces cerevisiae)
Spliceosome immediately after branching (2 MDa, Complex from Saccharomyces cerevisiae)
U2 snrna (small nuclear rna) (376 kDa, RNA from Saccharomyces cerevisiae)
Pre-mrna-splicing factor cwc25 (20 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae)
U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae)
U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae)
Unknown (16 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae)
Guanosine-5'-triphosphate (523 Da, Ligand)
Pre-mrna-splicing factor atp-dependent rna helicase prp16 (121 kDa, Protein from Saccharomyces cerevisiae)
Exon 1 (5' exon) of ubc4 pre-mrna (5 kDa, RNA from Saccharomyces cerevisiae)
U5 snrna (small nuclear rna) (57 kDa, RNA from Saccharomyces cerevisiae)
Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing helicase brr2 (246 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor clf1 (82 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-processing factor 19 (56 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor snt309 (20 kDa, Protein from Saccharomyces cerevisiae)
Intron of ubc4 pre-mrna (24 kDa, RNA from Saccharomyces cerevisiae)
Pre-mrna-splicing factor syf1 (100 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
Protein cwc16 (32 kDa, Protein from Saccharomyces cerevisiae)
Magnesium ion (24 Da, Ligand)
U6 snrna (small nuclear rna) (35 kDa, RNA from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae)
Cwc22 (69 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
Zinc ion (65 Da, Ligand)
Cwc15 (19 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)

[Show more]

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Showing 1 - 5 of 5. Page 1 of 1

Display: Statistics

Download

Select database:

EMDB [5]

Format:

Select the script type:

Shell (Unix-based) Batch (Windows-based)

Preview first 10

Field: