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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:

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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 xref_links:"interpro" AND resolution:[6 TO 8}

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EMD-11695

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Human pre-Bact-1 spliceosome

Release date: Dec. 23, 2020
Resolution: 7.8 Å
EM Method: Single-particle
Fitted PDBs: 7abg
Q-score: 0.147

Townsend C, Leelaram MN, Agafonov DE, Dybkov O, Will CL, Bertram K, Urlaub H, Kastner B, Stark H, Luhrmann R

Science (2020) 370 [ DOI: doi:10.1126/science.abc3753 Pubmed: 33243851 ]

Sample:

Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
Protein bud31 homolog (17 kDa, Protein from Homo sapiens)
U5 snrna (36 kDa, RNA from Homo sapiens)
Nuclear cap-binding protein subunit 1 (91 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 3 (135 kDa, Protein from Homo sapiens)
Transcription elongation regulator 1 (124 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 4 (44 kDa, Protein from Homo sapiens)
7-methyl-guanosine-5'-triphosphate-5'-guanosine (803 Da, Ligand)
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)
Smad nuclear-interacting protein 1 (45 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 6 (14 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)
Magnesium ion (24 Da, Ligand)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein 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)
Nuclear cap-binding protein subunit 2 (18 kDa, Protein from Homo sapiens)
Pleiotropic regulator 1 (57 kDa, Protein from Homo sapiens)
Snw domain-containing protein 1 (61 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)
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)
Ww domain-binding protein 11 (70 kDa, Protein from Homo sapiens)
Serine/arginine repetitive matrix protein 1 (102 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)
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)
Serine/arginine-rich splicing factor 1 (27 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)
U6 snrna (34 kDa, RNA from Homo sapiens)
Pre-bact-1 spliceosomal complex (Complex)
Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from Homo sapiens)
Inositol hexakisphosphate (660 Da, Ligand)
Phd finger-like domain-containing protein 5a (12 kDa, Protein from Homo sapiens)
U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Homo sapiens)
U2 snrna (60 kDa, RNA from Homo sapiens)
Pre-bact-1 spliceosomal complex (Complex from Homo sapiens)
Minx m3 pre-mrna (73 kDa, RNA from synthetic construct)
Guanosine-5'-triphosphate (523 Da, Ligand)
U6 snrna-associated sm-like protein lsm2 (10 kDa, Protein from Homo sapiens)

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EMD-10689

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human 17S U2 snRNP

Release date: June 17, 2020
Resolution: 7.1 Å
EM Method: Single-particle
Fitted PDBs: 6y53
Q-score: 0.057

Zhang Z, Will CL, Bertram K, Dybkov O, Hartmuth K, Agafonov DE, Hofele R, Urlaub H, Kastner B, Luhrmann R, Stark H

Nature (2020) 583 pp. 310-313 [ Pubmed: 32494006 DOI: doi:10.1038/s41586-020-2344-3 ]

Sample:

Small nuclear ribonucleoprotein sm d2 (13 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)
Probable atp-dependent rna helicase ddx46 (117 kDa, Protein from Homo sapiens)
Hiv tat-specific factor 1 (85 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)
Splicing factor 3b subunit 1 (146 kDa, Protein from Homo sapiens)
Splicing factor 3a subunit 2 (49 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)
Splicing factor 3a subunit 1 (88 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
Human 17s u2 snrnp (Complex from Homo sapiens)
U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Homo sapiens)
U2 snrna (60 kDa, RNA from Homo sapiens)

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EMD-6890

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Cryo-EM structure of the human activated spliceosome (late Bact) at 6.5 angstrom

Release date: Sept. 19, 2018
Resolution: 6.5 Å
EM Method: Single-particle
Fitted PDBs: 5z57
Q-score: 0.097

Zhang X, Yan C, Zhan X, Li L, Lei J, Shi Y

Cell Res (2018) 28 pp. 307-322 [ Pubmed: 29360106 DOI: doi:10.1038/cr.2018.14 ]

Sample:

Peptidyl-prolyl cis-trans isomerase e (33 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
Protein bud31 homolog (17 kDa, Protein from Homo sapiens)
Bud13 homolog (70 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)
Cell division cycle 5-like protein (92 kDa, Protein from Homo sapiens)
Smad nuclear-interacting protein 1 (45 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 6 (14 kDa, Protein from Homo sapiens)
Crooked neck-like protein 1 (100 kDa, Protein from Homo sapiens)
Alanine (89 Da, Ligand)
Pre-mrna-splicing factor atp-dependent rna helicase dhx16 (119 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)
U5 snrna (37 kDa, RNA from Homo sapiens)
Intron-binding protein aquarius (171 kDa, Protein from Homo sapiens)
Pleiotropic regulator 1 (57 kDa, Protein from Homo sapiens)
Rna-binding motif protein, x-linked 2 (37 kDa, Protein from Homo sapiens)
U6 snrna (34 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)
Pre-mrna-splicing factor rbm22 (46 kDa, Protein from Homo sapiens)
Skip (62 kDa, Protein 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 3a subunit 3 (58 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 2 (100 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)
Pre-mrna (87 kDa, RNA from unidentified adenovirus)
Small nuclear ribonucleoprotein f (9 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)
Inositol hexakisphosphate (660 Da, Ligand)
Small nuclear ribonucleoprotein-associated proteins b and b' (23 kDa, Protein from Homo sapiens)
Phd finger-like domain-containing protein 5a (12 kDa, Protein from Homo sapiens)
U2 snrna (60 kDa, RNA from Homo sapiens)
U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Homo sapiens)
Pre-mrna-splicing factor spf27 (26 kDa, Protein from Homo sapiens)
Guanosine-5'-triphosphate (523 Da, Ligand)
Late bact splieosome (Complex from Homo sapiens)
Pre-mrna-splicing factor cwc22 homolog (105 kDa, Protein from Homo sapiens)

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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:

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

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EMDB [4]

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