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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

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and development of technology

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new instruments and methods

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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_orcid:"0000-0003-1785-6510"

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EMD-4658

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Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution.

Release date: April 17, 2019
Resolution: 2.92 Å
EM Method: Single-particle
Fitted PDBs: 6qw6
Q-score: 0.361

Charenton C, Wilkinson ME, Nagai K

Science (2019) 364 pp. 362-367 [ DOI: doi:10.1126/science.aax3289 Pubmed: 30975767 ]

Sample:

U5 small nuclear ribonucleoprotein 40 kda protein (39 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
Pre-mrna-processing-splicing factor 8 (271 kDa, Protein from Homo sapiens)
116 kda u5 small nuclear ribonucleoprotein component (95 kDa, Protein from Homo sapiens)
U4/u6.u5 tri-snrnp-associated protein 2 (64 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm7 (11 kDa, Protein from Homo sapiens)
Human u4/u6.u5 tri-snrnp (1 MDa, Complex)
U5 small nuclear ribonucleoprotein 200 kda helicase (244 kDa, Protein from Homo sapiens)
U5.u4/u6 tri-snrnp (Complex from Homo sapiens)
Probable atp-dependent rna helicase ddx23 (Complex from Homo sapiens)
U6 snrna-associated sm-like protein lsm4 (15 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm3 (11 kDa, Protein from Homo sapiens)
Pre-mrna-processing factor 6 (107 kDa, Protein from Homo sapiens)
Guanosine-5'-triphosphate (523 Da, Ligand)
Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
U4/u6 small nuclear ribonucleoprotein prp3 (77 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm6 (9 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
Rna-binding protein 42 (50 kDa, Protein from Homo sapiens)
U4/u6 small nuclear ribonucleoprotein prp4 (58 kDa, Protein from Homo sapiens)
U4/u6 small nuclear ribonucleoprotein prp31 (55 kDa, Protein from Homo sapiens)
Probable atp-dependent rna helicase ddx23 (95 kDa, Protein from Homo sapiens)
U5 snrna (37 kDa, RNA from Homo sapiens)
Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
Nhp2-like protein 1 (14 kDa, Protein from Homo sapiens)
U6 snrna (28 kDa, RNA from Homo sapiens)
U6 snrna-associated sm-like protein lsm5 (9 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm8 (10 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
U4/u6.u5 small nuclear ribonucleoprotein 27 kda protein (18 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
Inositol hexakisphosphate (660 Da, Ligand)
U4 snrna (46 kDa, RNA from Homo sapiens)
Zinc ion (65 Da, Ligand)
Thioredoxin-like protein 4a (16 kDa, Protein from Homo sapiens)
U4/u6.u5 tri-snrnp-associated protein 1 (90 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm2 (10 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Homo sapiens)

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EMD-4665

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Structure of a human fully-assembled precatalytic spliceosome (pre-B complex).

Release date: April 17, 2019
Resolution: 3.28 Å
EM Method: Single-particle
Fitted PDBs: 6qx9
Q-score: 0.207

Charenton C, Wilkinson ME, Nagai K

Science (2019) 364 pp. 362-367 [ DOI: doi:10.1126/science.aax3289 Pubmed: 30975767 ]

Sample:

Splicing factor 3b subunit 4 (44 kDa, Protein from Homo sapiens)
U5 small nuclear ribonucleoprotein 40 kda protein (39 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
Pre-mrna-processing-splicing factor 8 (271 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 1 (146 kDa, Protein from Homo sapiens)
U4/u6.u5 tri-snrnp-associated protein 2 (64 kDa, Protein from Homo sapiens)
Splicing factor 3a subunit 3 (58 kDa, Protein from Homo sapiens)
U1 small nuclear ribonucleoprotein c (17 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm7 (11 kDa, Protein from Homo sapiens)
Splicing factor 3a subunit 1,splicing factor 3a subunit 1,splicing factor 3a subunit 1 (71 kDa, Protein from Homo sapiens)
116 kda u5 small nuclear ribonucleoprotein component (95 kDa, Protein from Homo sapiens)
U5 small nuclear ribonucleoprotein 200 kda helicase (244 kDa, Protein from Homo sapiens)
Probable atp-dependent rna helicase ddx23 (Complex from Homo sapiens)
U6 snrna-associated sm-like protein lsm4 (15 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm3 (11 kDa, Protein from Homo sapiens)
U6 snrna (34 kDa, RNA from Homo sapiens)
Guanosine-5'-triphosphate (523 Da, Ligand)
Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
U4/u6 small nuclear ribonucleoprotein prp3 (77 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm6 (9 kDa, Protein from Homo sapiens)
Serine/threonine-protein kinase prp4 homolog (117 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
Rna-binding protein 42 (50 kDa, Protein from Homo sapiens)
U4/u6 small nuclear ribonucleoprotein prp4 (58 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 5 (10 kDa, Protein from Homo sapiens)
U2 snrna (60 kDa, RNA from Homo sapiens)
Phd finger-like domain-containing protein 5a (11 kDa, Protein from Homo sapiens)
U4/u6 small nuclear ribonucleoprotein prp31 (55 kDa, Protein from Homo sapiens)
Splicing factor 3a subunit 2 (24 kDa, Protein from Homo sapiens)
U5 snrna (37 kDa, RNA from Homo sapiens)
Probable atp-dependent rna helicase ddx23 (95 kDa, Protein from Homo sapiens)
U1 small nuclear ribonucleoprotein a (31 kDa, Protein from Homo sapiens)
U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Homo sapiens)
Adml pre-mrna (15 kDa, RNA from Human adenovirus 2)
U2 small nuclear ribonucleoprotein b'' (25 kDa, Protein from Homo sapiens)
Adml pre-mrna (Complex from Human adenovirus 2)
Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 2 (100 kDa, Protein from Homo sapiens)
Nhp2-like protein 1 (14 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm8 (10 kDa, Protein from Homo sapiens)
U6 snrna-associated sm-like protein lsm5 (9 kDa, Protein from Homo sapiens)
Fully-assembled precatalytic spliceosome (pre-b complex). (Complex from Homo sapiens)
U1 small nuclear ribonucleoprotein 70 kda (51 kDa, Protein from Homo sapiens)
U4/u6.u5 small nuclear ribonucleoprotein 27 kda protein (18 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
Pre-mrna-processing factor 6 (97 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
Inositol hexakisphosphate (660 Da, Ligand)
U4 snrna (46 kDa, RNA from Homo sapiens)
Zinc ion (65 Da, Ligand)
Thioredoxin-like protein 4a (16 kDa, Protein from Homo sapiens)
U1 snrna (52 kDa, RNA from Homo sapiens)
U4/u6.u5 tri-snrnp-associated protein 1 (90 kDa, Protein from Homo sapiens)
Fully-assembled precatalytic spliceosome (pre-b complex). (3 MDa, Complex)
U6 snrna-associated sm-like protein lsm2 (10 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 3 (135 kDa, Protein from Homo sapiens)
Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Homo sapiens)

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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)

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