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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:"SmD2" AND author_name:"V" AND resolution:[5 TO 6}

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EMD-18788

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Cryo-EM structure of the cross-exon pre-B+5'ss complex

Release date: May 22, 2024
Resolution: 5.8 Å
EM Method: Single-particle
Fitted PDBs: 8r0a
Q-score: 0.102

Zhang Z, Kumar V, Dybkov O, Will CL, Zhong J, Ludwig SEJ, Urlaub H, Kastner B, Stark H, Luhrmann R

Nature (2024) 630 pp. 1012-1019 [ DOI: doi:10.1038/s41586-024-07458-1 Pubmed: 38778104 ]

Sample:

5'ss oligo (3 kDa, RNA from Homo sapiens)
Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
Ubiquitin carboxyl-terminal hydrolase 39 (65 kDa, Protein from Homo sapiens)
U4 snrna (46 kDa, RNA from Homo sapiens)
U4/u6 small nuclear ribonucleoprotein prp31 (55 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 3 (135 kDa, Protein from Homo sapiens)
U4/u6 small nuclear ribonucleoprotein prp4 (58 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 4 (44 kDa, Protein from Homo sapiens)
U2 small nuclear ribonucleoprotein b'' (25 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 6 (14 kDa, Protein from Homo sapiens)
Nhp2-like protein 1, n-terminally processed (14 kDa, Protein from Homo sapiens)
Thioredoxin-like protein 4a (16 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm3 (11 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm6 (9 kDa, Protein from Homo sapiens)
Pre-mrna-processing factor 6 (107 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm7 (11 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm4 (15 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm5 (9 kDa, Protein from Homo sapiens)
116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 1 (146 kDa, Protein from Homo sapiens)
U4/u6 small nuclear ribonucleoprotein prp3 (77 kDa, Protein from Homo sapiens)
U5 snrna (37 kDa, RNA from Homo sapiens)
Pre-mrna (111 kDa, RNA from Homo sapiens)
Splicing factor 3a subunit 2 (49 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 5 (10 kDa, Protein from Homo sapiens)
Rna-binding protein 42 (50 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm8 (10 kDa, Protein from Homo sapiens)
U5 small nuclear ribonucleoprotein 40 kda protein (39 kDa, Protein from Homo sapiens)
Splicing factor 3a subunit 3 (58 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 2 (100 kDa, Protein from Homo sapiens)
Probable atp-dependent rna helicase ddx23 (95 kDa, Protein from Homo sapiens)
U4/u6.u5 tri-snrnp-associated protein 1 (90 kDa, Protein from Homo sapiens)
Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from Homo sapiens)
Splicing factor 3a subunit 1 (88 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
U5 small nuclear ribonucleoprotein 200 kda helicase (244 kDa, Protein from Homo sapiens)
Serine/threonine-protein kinase prp4 homolog (117 kDa, Protein from Homo sapiens)
U6 snrna (34 kDa, RNA from Homo sapiens)
Phd finger-like domain-containing protein 5a (12 kDa, Protein from Homo sapiens)
U2 snrna (60 kDa, RNA from Homo sapiens)
Human spliceosomal pre-b+5'ss complex (Complex from Homo sapiens)
U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm2 (10 kDa, Protein from Homo sapiens)
U4/u6.u5 small nuclear ribonucleoprotein 27 kda protein (18 kDa, Protein from Homo sapiens)

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EMD-18529

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Cryo-EM structure of a human spliceosomal B complex protomer

Release date: Jan. 24, 2024
Resolution: 5.29 Å
EM Method: Single-particle
Fitted PDBs: 8qo9
Q-score: 0.158

Zhang Z, Kumar V, Dybkov O, Will CL, Urlaub H, Stark H, Luhrmann R

EMBO J (2024) 43 pp. 1065-1088 [ Pubmed: 38383864 DOI: doi:10.1038/s44318-024-00052-1 ]

Sample:

Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
Protein bud31 homolog (17 kDa, Protein from Homo sapiens)
U4 snrna (46 kDa, RNA from Homo sapiens)
U4/u6 small nuclear ribonucleoprotein prp31 (55 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 3 (135 kDa, Protein from Homo sapiens)
Wd40 repeat-containing protein smu1 (57 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 4 (44 kDa, Protein from Homo sapiens)
U2 snrna (60 kDa, RNA from Homo sapiens)
U4/u6 small nuclear ribonucleoprotein prp4 (58 kDa, Protein from Homo sapiens)
Transcription elongation regulator 1 (124 kDa, Protein from Homo sapiens)
U2 small nuclear ribonucleoprotein b'' (25 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 6 (14 kDa, Protein from Homo sapiens)
Thioredoxin-like protein 4a (16 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm3 (11 kDa, Protein from Homo sapiens)
Nhp2-like protein 1, n-terminally processed (14 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm6 (9 kDa, Protein from Homo sapiens)
Pre-mrna-processing factor 6 (107 kDa, Protein from Homo sapiens)
Human spliceosomal b complex (Complex from Homo sapiens)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
Protein red (65 kDa, Protein from Homo sapiens)
Minx pre-mrna (111 kDa, RNA from Homo sapiens)
U6 snrna-associated sm-like protein lsm7 (11 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm4 (15 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm5 (9 kDa, Protein from Homo sapiens)
116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 1 (146 kDa, Protein from Homo sapiens)
Ww domain-binding protein 4 (42 kDa, Protein from Homo sapiens)
U4/u6 small nuclear ribonucleoprotein prp3 (77 kDa, Protein from Homo sapiens)
U5 snrna (37 kDa, RNA from Homo sapiens)
Splicing factor 3b subunit 5 (10 kDa, Protein from Homo sapiens)
Splicing factor 3a subunit 2 (49 kDa, Protein from Homo sapiens)
Zinc finger matrin-type protein 2 (23 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm8 (10 kDa, Protein from Homo sapiens)
U5 small nuclear ribonucleoprotein 40 kda protein (39 kDa, Protein from Homo sapiens)
Microfibrillar-associated protein 1 (52 kDa, Protein from Homo sapiens)
Ubiquitin-like protein 5 (8 kDa, Protein from Homo sapiens)
Splicing factor 3a subunit 3 (58 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 2 (100 kDa, Protein from Homo sapiens)
U4/u6.u5 tri-snrnp-associated protein 1 (90 kDa, Protein from Homo sapiens)
Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from Homo sapiens)
Pre-mrna-splicing factor 38a (37 kDa, Protein from Homo sapiens)
Splicing factor 3a subunit 1 (88 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
Serine/arginine-rich splicing factor 1 (27 kDa, Protein from Homo sapiens)
U5 small nuclear ribonucleoprotein 200 kda helicase (244 kDa, Protein from Homo sapiens)
Peptidyl-prolyl cis-trans isomerase h (19 kDa, Protein from Homo sapiens)
U6 snrna (34 kDa, RNA from Homo sapiens)
Phd finger-like domain-containing protein 5a (12 kDa, Protein from Homo sapiens)
U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm2 (10 kDa, Protein from Homo sapiens)

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EMD-16658

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Structure of a late-stage activated spliceosome (BAqr) arrested with a dominant-negative Aquarius mutant (state B complex).

Release date: May 10, 2023
Resolution: 5.9 Å
EM Method: Single-particle
Fitted PDBs: 8ch6
Q-score: 0.154

Schmitzova J, Cretu C, Dienemann C, Urlaub H, Pena V

Nature (2023) 617 pp. 842-850 [ Pubmed: 37165190 DOI: doi:10.1038/s41586-023-06049-w ]

Sample:

Peptidyl-prolyl cis-trans isomerase e (33 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
G-patch domain and kow motifs-containing protein (52 kDa, Protein from Homo sapiens)
Bud13 homolog (70 kDa, Protein from Homo sapiens)
Protein bud31 homolog (17 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 3 (135 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 4 (44 kDa, Protein from Homo sapiens)
U2 small nuclear ribonucleoprotein b'' (25 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Homo sapiens)
Cell division cycle 5-like protein (92 kDa, Protein from Homo sapiens)
Crooked neck-like protein 1 (100 kDa, Protein from Homo sapiens)
Ring-type e3 ubiquitin-protein ligase ppil2 (58 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
Pre-mrna-processing factor 17 (65 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
Pre-mrna-splicing factor syf1 (100 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
Pre-mrna-processing factor 19 (55 kDa, Protein from Homo sapiens)
116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 1 (146 kDa, Protein from Homo sapiens)
Intron-binding protein aquarius (171 kDa, Protein from Homo sapiens)
Pleiotropic regulator 1 (57 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 5 (10 kDa, Protein from Homo sapiens)
Splicing factor 3a subunit 2 (49 kDa, Protein from Homo sapiens)
Pre-mrna-splicing factor rbm22 (46 kDa, Protein from Homo sapiens)
Rnu6-1 (34 kDa, RNA from Homo sapiens)
Rnu2-1 (60 kDa, RNA from Homo sapiens)
Serine/arginine repetitive matrix protein 2 (300 kDa, Protein from Homo sapiens)
Peptidyl-prolyl cis-trans isomerase-like 1 (18 kDa, Protein from Homo sapiens)
U5 small nuclear ribonucleoprotein 40 kda protein (39 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
Splicing factor 3b subunit 2 (100 kDa, Protein from Homo sapiens)
Splicing factor 3a subunit 3 (58 kDa, Protein from Homo sapiens)
Late human activated spliceosome arrested with a dominant-negative mutant of the splicing helicase aquarius (aquarius k829a) (Complex from Homo sapiens)
Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from Homo sapiens)
Putative pre-mrna-splicing factor atp-dependent rna helicase dhx16 (119 kDa, Protein from Homo sapiens)
Splicing factor 3a subunit 1 (88 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
Peptidyl-prolyl cis-trans isomerase-like 4 (57 kDa, Protein from Homo sapiens)
Ring finger protein 113a (38 kDa, Protein from Homo sapiens)
U5 small nuclear ribonucleoprotein 200 kda helicase (244 kDa, Protein from Homo sapiens)
Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from Homo sapiens)
Pre-mrna-splicing factor isy1 homolog (33 kDa, Protein from Homo sapiens)
Rnu5a-1 (37 kDa, RNA from Homo sapiens)
Inositol hexakisphosphate (660 Da, Ligand)
Phd finger-like domain-containing protein 5a (12 kDa, Protein from Homo sapiens)
Pre-mrna-splicing factor spf27 (26 kDa, Protein from Homo sapiens)
Minx-m3 (102 kDa, RNA from unidentified adenovirus)
U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Homo sapiens)
Guanosine-5'-triphosphate (523 Da, Ligand)
Snw domain-containing protein 1 (61 kDa, Protein from Homo sapiens)
Pre-mrna-splicing factor cwc22 homolog (105 kDa, Protein from Homo sapiens)

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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 [ Pubmed: 34349264 DOI: doi:10.1038/s41586-021-03789-5 ]

Sample:

Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor rds3 (12 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
Rds3 complex subunit 10 (10 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)
Protein luc7 (30 kDa, Protein from Saccharomyces cerevisiae)
U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
Cold sensitive u2 snrna suppressor 1 (50 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-processing protein prp40 (69 kDa, Protein from Saccharomyces cerevisiae)
Act1 pre-mrna (delta bs-a) (111 kDa, RNA 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)
Pre-mrna-splicing factor prp11 (31 kDa, Protein 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)
U2 snrnp component hsh155 (110 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor prp9 (63 kDa, Protein from Saccharomyces cerevisiae)
U1 snrna (182 kDa, RNA from Saccharomyces cerevisiae)
S. cerevisiae spliceosomal pre-a complex (Complex from Saccharomyces cerevisiae)
Pre-mrna-processing atp-dependent rna helicase prp5 (96 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
U1 small nuclear ribonucleoprotein 70 kda homolog (34 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)
U1 small nuclear ribonucleoprotein a (34 kDa, Protein from Saccharomyces cerevisiae)

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