5GAM image
Deposition Date 2015-12-15
Release Date 2016-02-03
Last Version Date 2024-05-15
Entry Detail
PDB ID:
5GAM
Keywords:
Title:
Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor 8
Gene (Uniprot):PRP8
Chain IDs:B (auth: A)
Chain Length:735
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor SNU114
Gene (Uniprot):SNU114
Chain IDs:C
Chain Length:1008
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:U5 snRNA
Chain IDs:A (auth: U)
Chain Length:178
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:U6 snRNA, 5' end
Chain IDs:D (auth: W)
Chain Length:31
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein-associated protein B
Gene (Uniprot):SMB1
Chain IDs:E (auth: b)
Chain Length:196
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D3
Gene (Uniprot):SMD3
Chain IDs:J (auth: d)
Chain Length:101
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein E
Gene (Uniprot):SME1
Chain IDs:F (auth: e)
Chain Length:94
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein F
Gene (Uniprot):SMX3
Chain IDs:G (auth: f)
Chain Length:86
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein G
Gene (Uniprot):SMX2
Chain IDs:H (auth: g)
Chain Length:77
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D1
Gene (Uniprot):SMD1
Chain IDs:K (auth: h)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D2
Gene (Uniprot):SMD2
Chain IDs:L (auth: j)
Chain Length:110
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Unknown polypeptide
Chain IDs:I (auth: x)
Chain Length:18
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Ligand Molecules
Primary Citation
Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Angstrom resolution
Nature 530 298 302 (2016)
PMID: 26829225 DOI: 10.1038/nature16940

Abstact

U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led to an essentially complete atomic model comprising 30 proteins plus U4/U6 and U5 small nuclear RNAs (snRNAs). The structure reveals striking interweaving interactions of the protein and RNA components, including extended polypeptides penetrating into subunit interfaces. The invariant ACAGAGA sequence of U6 snRNA, which base-pairs with the 5'-splice site during catalytic activation, forms a hairpin stabilized by Dib1 and Prp8 while the adjacent nucleotides interact with the exon binding loop 1 of U5 snRNA. Snu114 harbours GTP, but its putative catalytic histidine is held away from the γ-phosphate by hydrogen bonding to a tyrosine in the amino-terminal domain of Prp8. Mutation of this histidine to alanine has no detectable effect on yeast growth. The structure provides important new insights into the spliceosome activation process leading to the formation of the catalytic centre.

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Disease

Primary Citation of related structures