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Structure paper

TitleCryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution.
Journal, issue, pagesNature, Vol. 530, Issue 7590, Page 298-302, Year 2016
Publish dateFeb 18, 2016
AuthorsThi Hoang Duong Nguyen / Wojciech P Galej / Xiao-Chen Bai / Chris Oubridge / Andrew J Newman / Sjors H W Scheres / Kiyoshi Nagai /
PubMed AbstractU4/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 ...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.
External linksNature / PubMed:26829225 / PubMed Central
MethodsEM (single particle)
Resolution3.6 - 4.6 Å
Structure data

EMDB-8006:
The open state of the yeast U4/U6.U5 tri-snRNP at 4.2 Angstrom
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-8007:
The closed state of the yeast spliceosomal U4/U6.U5 tri-snRNP at 4.3 Angstrom
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-8008:
Combined Body and arm regions of the yeast spliceosomal U4/U6.U5 tri-snRNP by masked classification and refinement-Class 1
Method: EM (single particle) / Resolution: 4.6 Å

EMDB-8009:
Combined Body and arm regions of the yeast spliceosomal U4/U6.U5 tri-snRNP by masked classification and refinement-Class 2
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-8010:
Combined Body and arm regions of the yeast spliceosomal U4/U6.U5 tri-snRNP by masked classification and refinement-Class 3
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-8011, PDB-5gam:
Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-8012, PDB-5gan:
The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-8013, PDB-5gao:
Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-8014, PDB-5gap:
Body region of the U4/U6.U5 tri-snRNP
Method: EM (single particle) / Resolution: 3.6 Å

Chemicals

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

Source
  • saccharomyces cerevisiae (baker's yeast)
  • Baker's yeast (baker's yeast)
Keywords(U4-U6.U5)tri-snRNP-specific protein, S cerevisiae / Base Pairing / Catalytic Domain / Cryoelectron Microscopy / DNA Helicases / Exons / Guanosine Triphosphate / HCS1 protein, S cerevisiae / Hydrogen Bonding / Models, Molecular / Nucleic Acid Conformation / PRP8 protein, S cerevisiae / RNA Splice Sites / RNA, Small Nuclear / Ribonucleoprotein, U4-U6 Small Nuclear / Ribonucleoprotein, U5 Small Nuclear / Ribonucleoproteins, Small Nuclear / SNU114 protein, S cerevisiae / Saccharomyces cerevisiae / Saccharomyces cerevisiae Proteins / Spliceosomes / U5 small nuclear RNA / TRANSCRIPTION / pre-mRNA splicing / snRNP / GTPase / U5 snRNA / Prp8 / spliceosome / U4/U6 snRNP / Brr2 / Snu114 / RNA-protein complex / U4/U6.U5 snRNP

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