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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 author_name:"K" AND xref_links:"go" AND resolution:[4 TO 5}

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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-3766

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Cryo-EM structure of a pre-catalytic human spliceosome primed for activation (B complex)

Release date: Aug. 16, 2017
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 5o9z
Q-score: 0.17

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

Cell (2017) 170 pp. 701-713.e11 [ Pubmed: 28781166 DOI: doi:10.1016/j.cell.2017.07.011 ]

Sample:

U4/u6 small nuclear ribonucleoprotein prp31 (55 kDa, Protein from Human)
Splicing factor 3b subunit 3 (sf3b3) (135 kDa, Protein from Human)
Splicing factor 3b subunit 1 (146 kDa, Protein from Human)
Homo sapiens u4a snrna (46 kDa, RNA from Human)
Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Human)
U4/u6.u5 tri-snrnp-associated protein 1 (90 kDa, Protein from Human)
116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from Human)
Phd finger-like domain-containing protein 5a (12 kDa, Protein from Human)
U4/u6 small nuclear ribonucleoprotein prp4 (58 kDa, Protein from Human)
U2 small nuclear ribonucleoprotein b'' (25 kDa, Protein from Human)
Zinc finger matrin-type protein 2 (23 kDa, Protein from Human)
Nhp2-like protein 1 (14 kDa, Protein from Human)
Pre-mrna-splicing factor 38a (37 kDa, Protein from Human)
Small nuclear ribonucleoprotein f (9 kDa, Protein from Human)
U6 snrna-associated sm-like protein lsm3 (11 kDa, Protein from Human)
U6 snrna-associated sm-like protein lsm5 (9 kDa, Protein from Human)
U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Human)
Protein red (65 kDa, Protein from Human)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Human)
Homo sapiens u5 a small nuclear rna (36 kDa, RNA from Human)
Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from Human)
Homo sapiens rna, u6 small nuclear 1 (rnu6-1), small nuclear rna (34 kDa, RNA from Human)
U5 small nuclear ribonucleoprotein 200 kda helicase (244 kDa, Protein from Human)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Human)
Peptidyl-prolyl cis-trans isomerase h (19 kDa, Protein from Human)
Minx pre-mrna (103 kDa, RNA from Human)
Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Human)
Ww domain-binding protein 4 (42 kDa, Protein from Human)
U6 snrna-associated sm-like protein lsm6 (9 kDa, Protein from Human)
Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Human)
U6 snrna-associated sm-like protein lsm2 (10 kDa, Protein from Human)
Microfibrillar-associated protein 1 (52 kDa, Protein from Human)
U6 snrna-associated sm-like protein lsm4 (15 kDa, Protein from Human)
Pre-mrna-processing factor 6 (107 kDa, Protein from Human)
Human b complex spliceosome, sharpened map, masked refinement (Complex from Homo sapiens)
Wd40 repeat-containing protein smu1 (57 kDa, Protein from Human)
Human gene for small nuclear rna u2 (snrna u2) (60 kDa, RNA from Human)
U6 snrna-associated sm-like protein lsm8 (10 kDa, Protein from Human)
U5 small nuclear ribonucleoprotein 40 kda protein (39 kDa, Protein from Human)
Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Human)
U4/u6 small nuclear ribonucleoprotein prp3 (77 kDa, Protein from Human)
Thioredoxin-like protein 4a (16 kDa, Protein from Human)
Splicing factor 3b subunit 5 (10 kDa, Protein from Human)
U6 snrna-associated sm-like protein lsm7 (11 kDa, Protein from Human)

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EMD-3541

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Structure of a spliceosome remodeled for exon ligation

Release date: Jan. 18, 2017
Resolution: 4.17 Å
EM Method: Single-particle
Fitted PDBs: 5mq0
Q-score: 0.223

Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ, Nagai K

Nature (2017) 542 pp. 377-380 [ DOI: doi:10.1038/nature21078 Pubmed: 28076345 ]

Sample:

Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
Potassium ion (39 Da, Ligand)
5'-exon of ubc4 pre-mrna (6 kDa, RNA from Saccharomyces cerevisiae)
Saccharomyces cerevisiae strain t.52_2h chromosome xii sequence (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)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae)
3'-exon of ubc4 pre-mrna, bound by prp22 helicase (873 Da, RNA from Saccharomyces cerevisiae)
Pre-mrna-splicing factor syf1,pre-mrna-splicing factor syf1 (101 kDa, Protein from Saccharomyces cerevisiae)
Magnesium ion (24 Da, Ligand)
Yeast ubc4 gene for ubiquitin-conjugating enzyme (30 kDa, RNA from Saccharomyces cerevisiae)
Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae)
S.cerevisiae chromosome ii reading frame orf ybr230c (376 kDa, RNA from Saccharomyces cerevisiae)
Saccharomyces cerevisiae strain wi_c_mbsp_4 chromosome vii sequence (57 kDa, RNA 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)
Unknown protein (5 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor slu7 (44 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-processing factor 17 (52 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)
Pre-mrna-splicing factor atp-dependent rna helicase prp22 (130 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor 18 (28 kDa, Protein from Saccharomyces cerevisiae)
Saccharomyces cerevisiae spliceosome. complex c just after prp16-mediated remodeling (Complex)
Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae)
Inositol hexakisphosphate (660 Da, Ligand)
Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
Guanosine-5'-triphosphate (523 Da, Ligand)
Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae)
U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor clf1 (82 kDa, Protein from Saccharomyces cerevisiae)

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EMD-8013

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Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP

Release date: Jan. 27, 2016
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 5gao
Q-score: 0.305

Nguyen TH, Galej WP, Bai XC, Oubridge C, Newman AJ, Scheres SH, Nagai K

Nature (2016) 530 pp. 298-302 [ Pubmed: 26829225 DOI: doi:10.1038/nature16940 ]

Sample:

Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
Saccharomyces cerevisiae strain uoa_m2 chromosome 5 sequence (30 kDa, RNA from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
Snu66 (25 kDa, Protein from Saccharomyces cerevisiae)
Pre-mrna-splicing factor 8 (30 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
Head region of the yeast spliceosomal u4/u6.u5 tri-snrnp (400 kDa, Complex from Saccharomyces cerevisiae)
Small nuclear ribonucleoprotein g (8 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)

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Sort by: Download

Showing 1 - 4 of 4. Page 1 of 1

Display: Statistics

Download

Select database:

EMDB [4]

Format:

Select the script type:

Shell (Unix-based) Batch (Windows-based)

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