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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

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offer vital services to scientists in the member states

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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:"Pre-mRNA-splicing factor PRP9" AND xref_links:"cpx"

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EMD-13028

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The U2 part of Saccharomyces cerevisiae spliceosomal pre-A complex (delta BS-A ACT1)

Release date: Aug. 11, 2021
Resolution: 9.0 Å
EM Method: Single-particle
Fitted PDBs: 7oqb
Q-score: 0.133

Zhang Z, Rigo N, Dybkov O, Fourmann JB, Will CL, Kumar V, Urlaub H, Stark H, Luhrmann R

Nature (2021) 596 pp. 296-300 [ DOI: doi:10.1038/s41586-021-03789-5 Pubmed: 34349264 ]

Sample:

U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor rse1 (153 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein-associated protein b (22 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)
Act1 pre-mrna (delta-bs-a) (101 kDa, RNA from Saccharomyces cerevisiae)
Pre-mrna-splicing factor rds3 (12 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-processing atp-dependent rna helicase prp5 (96 kDa, Protein from Saccharomyces cerevisiae)
U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae)
Cold sensitive u2 snrna suppressor 1 (50 kDa, Protein from Saccharomyces cerevisiae)
Rds3 complex subunit 10 (9 kDa, Protein from Saccharomyces cerevisiae)
U2 snrnp component hsh155 (110 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor prp9 (63 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor prp21 (33 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
Protein hsh49 (24 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
S. cerevisiae spliceosomal pre-a complex (Complex from Saccharomyces cerevisiae)
Pre-mrna-splicing factor prp11 (31 kDa, Protein from Saccharomyces cerevisiae)

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EMD-13033

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Saccharomyces cerevisiae spliceosomal pre-A complex (delta BS-A ACT1)

Release date: Aug. 11, 2021
Resolution: 5.9 Å
EM Method: Single-particle
Fitted PDBs: 7oqe
Q-score: 0.121

Zhang Z, Rigo N, Dybkov O, Fourmann JB, Will CL, Kumar V, Urlaub H, Stark H, Luhrmann R

Nature (2021) 596 pp. 296-300 [ DOI: doi:10.1038/s41586-021-03789-5 Pubmed: 34349264 ]

Sample:

56 kda u1 small nuclear ribonucleoprotein component (56 kDa, Protein from Saccharomyces cerevisiae)
Act1 pre-mrna (delta bs-a) (111 kDa, RNA from Saccharomyces cerevisiae)
U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae)
Protein nam8 (57 kDa, Protein from Saccharomyces cerevisiae)
U1 small nuclear ribonucleoprotein component snu71 (71 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor rse1 (153 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
U1 small nuclear ribonucleoprotein 70 kda homolog (34 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
Protein luc7 (30 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae)
U1 small nuclear ribonucleoprotein component prp42 (65 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-processing protein prp40 (69 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor rds3 (12 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-processing atp-dependent rna helicase prp5 (96 kDa, Protein from Saccharomyces cerevisiae)
Rds3 complex subunit 10 (10 kDa, Protein from Saccharomyces cerevisiae)
U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae)
Cold sensitive u2 snrna suppressor 1 (50 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor prp11 (31 kDa, Protein from Saccharomyces cerevisiae)
U2 snrnp component hsh155 (110 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor prp9 (63 kDa, Protein from Saccharomyces cerevisiae)
U1 small nuclear ribonucleoprotein c (27 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor prp21 (33 kDa, Protein from Saccharomyces cerevisiae)
Protein hsh49 (24 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-processing factor 39 (74 kDa, Protein from Saccharomyces cerevisiae)
S. cerevisiae spliceosomal pre-a complex (Complex from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
U1 small nuclear ribonucleoprotein a (34 kDa, Protein from Saccharomyces cerevisiae)
U1 snrna (182 kDa, RNA from Saccharomyces cerevisiae)

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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:

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

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EMD-3683

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Structure of a pre-catalytic spliceosome (B2 map)

Release date: May 31, 2017
Resolution: 7.2 Å
EM Method: Single-particle
Fitted PDBs: 5nrl
Q-score: 0.117

Plaschka C, Lin PC, Nagai K

Nature (2017) 546 pp. 617-621 [ Pubmed: 28530653 DOI: doi:10.1038/nature22799 ]

Sample:

66 kda u4/u6.u5 small nuclear ribonucleoprotein component (66 kDa, Protein from Saccharomyces cerevisiae)
U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae)
U6 snrna-associated sm-like protein lsm7 (13 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Guanosine-5'-triphosphate (523 Da, Ligand)
Pre-mrna-splicing factor prp11 (29 kDa, Protein from Saccharomyces cerevisiae)
U4 snrna (51 kDa, RNA from Saccharomyces cerevisiae)
Pre-mrna-splicing factor rse1 (153 kDa, Protein from Saccharomyces cerevisiae)
U6 snrna-associated sm-like protein lsm3 (10 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
U6 snrna-associated sm-like protein lsm8 (12 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor spp381 (33 kDa, Protein from Saccharomyces cerevisiae)
U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae)
Unknown (7 kDa, Protein from Saccharomyces cerevisiae)
U5 snrna (68 kDa, RNA from Saccharomyces cerevisiae)
Pre-mrna-splicing factor 38 (27 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor rds3 (12 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-processing factor 31 (56 kDa, Protein from Saccharomyces cerevisiae)
U6 snrna-associated sm-like protein lsm2 (11 kDa, Protein from Saccharomyces cerevisiae)
U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae)
Pre-catalytic b complex spliceosome (2 MDa, Complex from Saccharomyces cerevisiae)
Rds3 complex subunit 10 (10 kDa, Protein from Saccharomyces cerevisiae )
Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cold sensitive u2 snrna suppressor 1 (50 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae)
U6 snrna-associated sm-like protein lsm6 (9 kDa, Protein from Saccharomyces cerevisiae )
U2 snrnp component hsh155 (110 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor prp9 (63 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Zinc ion (65 Da, Ligand)
U4/u6 small nuclear ribonucleoprotein prp3 (55 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor prp21 (33 kDa, Protein from Saccharomyces cerevisiae)
Protein hsh49 (24 kDa, Protein from Saccharomyces cerevisiae)
U6 snrna-associated sm-like protein lsm5 (10 kDa, Protein from Saccharomyces cerevisiae)
U6 snrna (35 kDa, RNA from Saccharomyces cerevisiae)
13 kda ribonucleoprotein-associated protein (13 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
Yeast ubc4 gene for ubiquitin-conjugating enzyme (30 kDa, RNA from Saccharomyces cerevisiae)
U4/u6 small nuclear ribonucleoprotein prp4 (52 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing helicase brr2 (246 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
U6 snrna-associated sm-like protein lsm4 (21 kDa, Protein from Saccharomyces cerevisiae )
Spliceosomal protein dib1 (16 kDa, Protein from Saccharomyces cerevisiae)
23 kda u4/u6.u5 small nuclear ribonucleoprotein component (22 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor 6 (104 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))

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EMDB [4]

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