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EMBL

was set up in 1974 as Europe’s flagship laboratory for the life sciences – an intergovernmental organisation with more than 80 independent research groups covering the spectrum of molecular biology:

Research:

perform basic research in molecular biology

Services:

offer vital services to scientists in the member states

Training

scientists, students and visitors at all levels

Transfer

and development of technology

Develop

new instruments and methods

Integrating

life science research in Europe

More about EMBL

Six sites

represent EMBL in Europe.

Barcelona

Tissue biology and disease modelling

Grenoble

Structural biology

Hamburg

Structural biology

Heidelberg

Main laboratory

Hinxton

EMBL-EBI: European Bioinformatics Institute

Rome

Epigenetics and neurobiology

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sample_name:"SmD2" AND xref_links:"interpro" AND xref_links:"scop2" AND xref_links:"cath"

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EMD-0687

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Cryo-EM structure of the yeast B*-a1 complex at an average resolution of 3.6 angstrom

Release date: April 24, 2019
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6j6h
Q-score: 0.283

Wan R, Bai R, Yan C, Lei J, Shi Y

Cell (2019) 177 pp. 339-351.e13 [ Pubmed: 30879786 DOI: doi:10.1016/j.cell.2019.02.006 ]

Sample:

Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor syf1 (100 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae S288c)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Magnesium ion (24 Da, Ligand)
Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor cef1 (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor snt309 (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Zinc ion (65 Da, Ligand)
U5 snrna (68 kDa, RNA from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor clf1 (82 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
U6 snrna (35 kDa, RNA from Saccharomyces cerevisiae S288c)
Pre-mrna-processing factor 17 (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Catalytically activated spliceosome b*-a1 complex (Complex from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor isy1 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Inositol hexakisphosphate (660 Da, Ligand)
Guanosine-5'-triphosphate (523 Da, Ligand)
Act1 pre-mrna (217 kDa, RNA from Saccharomyces cerevisiae S288c)
Pre-mrna-processing factor 19 (56 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))

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EMD-4364

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Prespliceosome structure provides insight into spliceosome assembly and regulation (map A2)

Release date: Aug. 22, 2018
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6g90
Q-score: 0.152

Plaschka C, Lin PC, Charenton C, Nagai K

Nature (2018) 559 pp. 419-422 [ Pubmed: 29995849 DOI: doi:10.1038/s41586-018-0323-8 ]

Sample:

Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor rds3 (12 kDa, Protein from Saccharomyces cerevisiae)
Rds3 complex subunit 10 (10 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
U1 small nuclear ribonucleoprotein 70 kda homolog,u1 small nuclear ribonucleoprotein 70 kda homolog,u1 small nuclear ribonucleoprotein 70 kda homolog (33 kDa, Protein from Saccharomyces cerevisiae)
Protein hsh49 (24 kDa, Protein from Saccharomyces cerevisiae)
U1 small nuclear ribonucleoprotein c (27 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-processing factor 39 (74 kDa, Protein from Saccharomyces cerevisiae)
Prespliceosome a complex (1 MDa, Complex from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
Yeast ubc4 pre-mrna (mutant) (12 kDa, RNA from Saccharomyces cerevisiae)
U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor rse1 (153 kDa, Protein from Saccharomyces cerevisiae)
Protein nam8 (57 kDa, Protein from Saccharomyces cerevisiae)
56 kda u1 small nuclear ribonucleoprotein component (56 kDa, Protein from Saccharomyces cerevisiae)
U1 snrna,u1 snrna,u1 snrna,u1 snrna,u1 snrna (126 kDa, RNA from Saccharomyces cerevisiae)
U1 small nuclear ribonucleoprotein component snu71 (71 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor prp21 (33 kDa, Protein from Saccharomyces cerevisiae)
Unknown (4 kDa, Protein from Saccharomyces cerevisiae)
Zinc ion (65 Da, Ligand)
U2 snrnp component hsh155 (110 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
Cold sensitive u2 snrna suppressor 1 (50 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor prp9 (63 kDa, Protein from Saccharomyces cerevisiae)
U2 snrna (45 kDa, RNA from Saccharomyces cerevisiae)
Pre-mrna-splicing factor prp11,pre-mrna-splicing factor prp11,pre-mrna-splicing factor prp11 (29 kDa, Protein from Saccharomyces cerevisiae)
Protein luc7,protein luc7,protein luc7 (28 kDa, Protein from Saccharomyces cerevisiae)
U1 small nuclear ribonucleoprotein a,u1 small nuclear ribonucleoprotein a,u1 small nuclear ribonucleoprotein a,u1 small nuclear ribonucleoprotein a,u1 small nuclear ribonucleoprotein a (33 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
U1 small nuclear ribonucleoprotein component prp42 (65 kDa, Protein from Saccharomyces cerevisiae)
U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae)

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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:

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

[Show more]

EMD-9525

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Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 angstrom resolution

Release date: Aug. 17, 2016
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 5gmk
Q-score: 0.279

Wan R, Yan C, Bai R, Huang G, Shi Y

Science (2016) 353 pp. 895-904 [ Pubmed: 27445308 DOI: doi:10.1126/science.aag2235 ]

Sample:

Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae S288C)
U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae S288c)
Pre-mrna-processing factor 17 (52 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor syf1 (78 kDa, Protein from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor cef1 (61 kDa, Protein from Saccharomyces cerevisiae S288C)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae S288C)
Magnesium ion (24 Da, Ligand)
Pre-mrna-processing factor 19 (56 kDa, Protein from Saccharomyces cerevisiae S288C)
Spliceosomal c complex (Complex from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor snt309 (20 kDa, Protein from Saccharomyces cerevisiae S288C)
Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor clf1 (68 kDa, Protein from Saccharomyces cerevisiae S288C)
5'-exon (4 kDa, RNA from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae S288C)
Zinc ion (65 Da, Ligand)
U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae S288C)
U5 snrna (68 kDa, RNA from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor cwc25 (20 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor isy1 (28 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae S288C)
U6 snrna (35 kDa, RNA from Saccharomyces cerevisiae S288c)
5'-splicing site (4 kDa, RNA from Saccharomyces cerevisiae S288c)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae S288C)
Intron_bps (9 kDa, RNA from Saccharomyces cerevisiae S288c)
Guanosine-5'-triphosphate (523 Da, Ligand)
Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
Protein cwc16 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae S288C)

[Show more]

EMD-4055

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Overall map of the yeast spliceosome immediately after branching

Release date: Aug. 3, 2016
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 5lj3
Q-score: 0.328

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:

U5 snrna (small nuclear rna) (57 kDa, RNA from Saccharomyces cerevisiae)
U2 snrna (small nuclear rna) (376 kDa, RNA from Saccharomyces cerevisiae)
Exon 1 (5' exon) of ubc4 pre-mrna (5 kDa, RNA from Saccharomyces cerevisiae)
Cwc15 (19 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor cwc25 (20 kDa, Protein from Saccharomyces cerevisiae )
Cwc2 (38 kDa, Protein from Saccharomyces cerevisiae)
U6 snrna (small nuclear rna) (35 kDa, RNA from Saccharomyces cerevisiae)
Isy1 (28 kDa, Protein from Saccharomyces cerevisiae)
Magnesium ion (24 Da, Ligand)
Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae )
Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae )
Unknown (11 kDa, Protein from Saccharomyces cerevisiae)
Clf1 (82 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae )
Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae)
Cef1 (67 kDa, Protein from Saccharomyces cerevisiae)
U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae )
Zinc ion (65 Da, Ligand)
Intron of ubc4 pre-mrna (24 kDa, RNA from Saccharomyces cerevisiae)
Spliceosome immediately after branching (2 MDa, Complex from Saccharomyces cerevisiae)
Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae )
Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae )
Prp46 (50 kDa, Protein from Saccharomyces cerevisiae)
Protein cwc16 (32 kDa, Protein from Saccharomyces cerevisiae )
Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae )
Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
Cwc22 (69 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae )
Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae )
Guanosine-5'-triphosphate (523 Da, Ligand)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae )
U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae )
Syf1 (100 kDa, Protein from Saccharomyces cerevisiae)

[Show more]

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EMDB [5]

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