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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

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 xref_links:"scop2" AND author_name:"Yan"

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EMD-0687

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Cryo-EM structure of the yeast B*-a1 complex at an average resolution of 3.6 angstrom

Release date: April 24, 2019
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6j6h
Q-score: 0.283

Wan R, Bai R, Yan C, Lei J, Shi Y

Cell (2019) 177 pp. 339-351.e13 [ Pubmed: 30879786 DOI: doi:10.1016/j.cell.2019.02.006 ]

Sample:

Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor syf1 (100 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae S288c)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Magnesium ion (24 Da, Ligand)
Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor cef1 (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor snt309 (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Zinc ion (65 Da, Ligand)
U5 snrna (68 kDa, RNA from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor clf1 (82 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
U6 snrna (35 kDa, RNA from Saccharomyces cerevisiae S288c)
Pre-mrna-processing factor 17 (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Catalytically activated spliceosome b*-a1 complex (Complex from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor isy1 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Inositol hexakisphosphate (660 Da, Ligand)
Guanosine-5'-triphosphate (523 Da, Ligand)
Act1 pre-mrna (217 kDa, RNA from Saccharomyces cerevisiae S288c)
Pre-mrna-processing factor 19 (56 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))

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EMD-6891

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Cryo-EM structure of a human activated spliceosome (early Bact) at 4.9 angstrom.

Release date: Sept. 19, 2018
Resolution: 4.9 Å
EM Method: Single-particle
Fitted PDBs: 5z58
Q-score: 0.131

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:

Small nuclear ribonucleoprotein sm d2 (13 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)
Pre-mrna-splicing factor atp-dependent rna helicase dhx16 (119 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
Early bact spliceosome (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)
Small nuclear ribonucleoprotein sm d3 (13 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)
Rna-binding motif protein, x-linked 2 (37 kDa, Protein from Homo sapiens)
Pleiotropic regulator 1 (57 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)
Skip (62 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)
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)
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)
Peptidyl-prolyl cis-trans isomerase cwc27 homolog (53 kDa, Protein from Homo sapiens)
Guanosine-5'-triphosphate (523 Da, Ligand)
Pre-mrna-splicing factor cwc22 homolog (105 kDa, Protein from Homo sapiens)

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EMD-6972

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Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.4~4.6 angstrom (tri-snRNP and U2 snRNP Part)

Release date: Aug. 29, 2018
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 5zwm
Q-score: 0.162

Bai R, Wan R, Yan C, Lei J, Shi Y

Science (2018) 360 pp. 1423-1429 [ DOI: doi:10.1126/science.aau0325 Pubmed: 29794219 ]

Sample:

Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae S288c)
Yeast fully assembled spliceosomal pre-b complex before activation (Cell from Saccharomyces cerevisiae)
U6 snrna (35 kDa, RNA from Saccharomyces cerevisiae S288c)
Pre-mrna-bps (13 kDa, RNA from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor prp11 (29 kDa, Protein from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor 6 (104 kDa, Protein from Saccharomyces cerevisiae S288c)
Rds3 complex subunit 10 (10 kDa, Protein from Saccharomyces cerevisiae S288c)
Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae S288c)
U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae S288c)
U6 snrna-associated sm-like protein lsm4 (21 kDa, Protein from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing helicase brr2 (246 kDa, Protein from Saccharomyces cerevisiae S288c)
Magnesium ion (24 Da, Ligand)
Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae S288c)
Cold sensitive u2 snrna suppressor 1 (50 kDa, Protein from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor prp9 (63 kDa, Protein from Saccharomyces cerevisiae S288c)
Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae S288c)
U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae S288c)
U4/u6 small nuclear ribonucleoprotein prp4 (52 kDa, Protein from Saccharomyces cerevisiae S288c)
66 kda u4/u6.u5 small nuclear ribonucleoprotein component (66 kDa, Protein from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor rds3 (12 kDa, Protein from Saccharomyces cerevisiae S288c)
Zinc ion (65 Da, Ligand)
Pre-mrna-processing factor 31 (56 kDa, Protein from Saccharomyces cerevisiae S288c)
U5 snrna (68 kDa, RNA from Saccharomyces cerevisiae S288c)
U6 snrna-associated sm-like protein lsm7 (13 kDa, Protein from Saccharomyces cerevisiae S288c)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae S288c)
U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae S288c)
Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae S288c)
Pre-mrna leakage protein 1 (23 kDa, Protein from Saccharomyces cerevisiae S288c)
U6 snrna-associated sm-like protein lsm5 (10 kDa, Protein from Saccharomyces cerevisiae S288c)
U6 snrna-associated sm-like protein lsm2 (11 kDa, Protein from Saccharomyces cerevisiae S288c)
U4 snrna (51 kDa, RNA from Saccharomyces cerevisiae S288c)
Spliceosomal protein dib1 (16 kDa, Protein from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor rse1 (153 kDa, Protein from Saccharomyces cerevisiae S288c)
U6 snrna-associated sm-like protein lsm8 (12 kDa, Protein from Saccharomyces cerevisiae S288c)
U6 snrna-associated sm-like protein lsm6 (9 kDa, Protein from Saccharomyces cerevisiae S288c)
Protein hsh49 (24 kDa, Protein from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor cwc26 (30 kDa, Protein from Saccharomyces cerevisiae S288c)
U4/u6 small nuclear ribonucleoprotein prp3 (55 kDa, Protein from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor prp21 (33 kDa, Protein from Saccharomyces cerevisiae S288c)
U2 snrnp component ist3 (17 kDa, Protein from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae S288c)
U2 snrnp component hsh155 (110 kDa, Protein from Saccharomyces cerevisiae S288c)
Guanosine-5'-triphosphate (523 Da, Ligand)
Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae S288c)
Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae S288c)
U6 snrna-associated sm-like protein lsm3 (10 kDa, Protein from Saccharomyces cerevisiae S288c)
13 kda ribonucleoprotein-associated protein (13 kDa, Protein from Saccharomyces cerevisiae S288c)

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EMD-6721

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Cryo-EM structure of the human spliceosome just prior to exon ligation at 3.6 angstrom

Release date: July 5, 2017
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 5xjc
Q-score: 0.22

Zhang X, Yan C, Hang J, Finci LI, Lei J, Shi Y

Cell (2017) 169 pp. 918-929.e14 [ Pubmed: 28502770 DOI: doi:10.1016/j.cell.2017.04.033 ]

Sample:

Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
Protein bud31 homolog (17 kDa, Protein from Homo sapiens)
Adenosine-5'-diphosphate (427 Da, Ligand)
Pre-mrna-splicing factor slu7 (68 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)
Crooked neck-like protein 1 (100 kDa, Protein from Homo sapiens)
Atp-dependent rna helicase dhx8 (139 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)
Pre-mrna (87 kDa, RNA from Human adenovirus 2)
116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from Homo sapiens)
Homo sapiens small nuclear rna (u2) gene (60 kDa, RNA 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)
Human c* spliceosome (Complex from Homo sapiens)
U6 snrna (34 kDa, RNA from Homo sapiens)
Pre-mrna-splicing factor syf2 (28 kDa, Protein from Homo sapiens)
Pre-mrna-splicing factor rbm22 (46 kDa, Protein from Homo sapiens)
Protein casc3 (76 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)
Snw domain-containing protein 1 (61 kDa, Protein from Homo sapiens)
Pre-mrna-processing-splicing factor 8 (273 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)
Adenosine-5'-triphosphate (507 Da, Ligand)
Rna-binding protein 8a (19 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)
Pre-mrna-splicing factor spf27 (26 kDa, Protein from Homo sapiens)
U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Homo sapiens)
Prkr-interacting protein 1 (21 kDa, Protein from Homo sapiens)
Guanosine-5'-triphosphate (523 Da, Ligand)
Eukaryotic initiation factor 4a-iii (46 kDa, Protein from Homo sapiens)
Protein mago nashi homolog 2 (17 kDa, Protein from Homo sapiens)
Pre-mrna-splicing factor cwc22 homolog (105 kDa, Protein from Homo sapiens)

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EMD-9525

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Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 angstrom resolution

Release date: Aug. 17, 2016
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 5gmk
Q-score: 0.279

Wan R, Yan C, Bai R, Huang G, Shi Y

Science (2016) 353 pp. 895-904 [ Pubmed: 27445308 DOI: doi:10.1126/science.aag2235 ]

Sample:

Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae S288C)
U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae S288c)
Pre-mrna-processing factor 17 (52 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor syf1 (78 kDa, Protein from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor cef1 (61 kDa, Protein from Saccharomyces cerevisiae S288C)
Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae S288C)
Magnesium ion (24 Da, Ligand)
Pre-mrna-processing factor 19 (56 kDa, Protein from Saccharomyces cerevisiae S288C)
Spliceosomal c complex (Complex from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor snt309 (20 kDa, Protein from Saccharomyces cerevisiae S288C)
Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor clf1 (68 kDa, Protein from Saccharomyces cerevisiae S288C)
5'-exon (4 kDa, RNA from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae S288C)
Zinc ion (65 Da, Ligand)
U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae S288C)
U5 snrna (68 kDa, RNA from Saccharomyces cerevisiae S288c)
Pre-mrna-splicing factor cwc25 (20 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor isy1 (28 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae S288C)
U6 snrna (35 kDa, RNA from Saccharomyces cerevisiae S288c)
5'-splicing site (4 kDa, RNA from Saccharomyces cerevisiae S288c)
Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae S288C)
Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae S288C)
Intron_bps (9 kDa, RNA from Saccharomyces cerevisiae S288c)
Guanosine-5'-triphosphate (523 Da, Ligand)
Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
Protein cwc16 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae S288C)

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EMDB [5]

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