Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution

Abstract

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.

Extended Data Figure 1. Image processing procedures

a, Representative micrograph. b, Representative 2D class averages obtained from reference-free 2D classification. c, Classification and refinement procedures used in this study.

Extended Data Figure 2. Local and overall resolutions of tri-snRNP maps

Local resolution estimation by Resmap of a, the overall 3.7 Å map and b, maps of thehead, body and foot domains obtained from masked refinements with signal subtraction. c, Gold-standard FSC curves for the overall map and the maps of the head, body and foot domains obtained from masked refinements. Their resolutions are estimated at FSC=0.143. d, e, f and g FSC curves of model versus map and cross-validation of model refinement by half-maps for the Body, Foot, Head and Overall maps, respectively. The red curves show FSC between the atomic model and the half-map it was refined against (half1) and the blue curves show FSC between the atomic model and the other half-map (half2) it was not refined against. The black curves show FSC between the atomic model and the sum map which the model was refined against.

Extended Data Figure 3. Representative EM density for different components of the map

a, Snu114 in the Foot domain with a bound GTP (magenta). The inset shows the GTP-binding pocket. b, Brr2 in the Head domain with a bound single-stranded region of U4 snRNA. The inset shows the density in the RNA binding tunnel. c, Density for Prp8 large and RNase-like domains. The inset shows the density in the core of Prp8. d, e and f, Prp3, Prp31 and Prp6 densities, respectively, with extended polypeptides.

Extended Data Figure 4. Secondary structure of the snRNAs in tri-snRNP

a, U4/U6 snRNA; c, U5 snRNA. The colored nucleotides with red, green and blue background were built de novo into our EM density. The region near the ACAGAGA sequence of U6 snRNA forms a stem-loop that was not predicted previously. b, d, Representative EM density for U4/U6 snRNA duplex and U5 snRNA, respectively.

Extended Data Figure 5. Interactions of Snu114 with guanine nucleotides and the N-terminal domain of Prp8 in the S. cerevisiae U4/U6.U5 tri-snRNP and S. pombe ILS complexes

a, Conformation of the Snu114(Cwf10)-bound GDP refined in the S. pombe ILS spliceosomal complex^, (red, PDB 3JB9), was overlaid on GDPs found in other guanine-nucleotide binding proteins (grey, PDB coordinates: 1DAR, 2E1R, 2WRI, 1Z0I, 5CA8, 1XTQ, 4YLG, 1SF8, 5BXQ). b, Guanine nucleotide refined as GDP in Snu114 of the S. cerevisiae U4/U6.U5 tri-snRNP (blue) is overlaid on GDPs found in the PDB coordinates as in a. c, Conformation of guanine nucleotide refined as GTP in Snu114 of the S. cerevisiae U4/U6.U5 tri-snRNP (blue) agrees well with GTP or GTP analogs in other guanine-nucleotide binding proteins (PDB code: 2BV3, 2DY1, 2J7K, 4YW9, 1ASO, 1LF0 (grey)). d, Superposition of the active site of Snu114-GTP and Cwf10-GDP. e, Superposition of the GDP-bound EF-G (2WRI), GMP-PCP bound EF-G (4JUW) and Snu114 (S. cerevisiae tri-snRNP) active sites. His218 (His78 in EF-G) positions water molecule crucial for GTP hydrolysis. f, Comparison of Prp8^N-term domain, Snu114 and U5 snRNA in the S. cerevisiae U4/U6.U5 complex and S. pombe ILS complex. g, Growth of serial dilutions of yeast strains carrying wild-type Snu114, His218Arg or His218Ala Snu114 mutants at different temperatures. Cells were spotted on YPD plates and grown at 14°C for 10 days, 30°C and 37°C for 2 days. h, Growth of serial dilutions of yeast strains carrying wild-type Prp8, Tyr403Phe and Tyr403Ala mutants. Cells were spotted on YPD plates and grown at 14°C for 9 days, 30°C for 3 days. This yeast strain does not survive at 37°C and thus is not shown.

Extended Data Figure 6. Conformational flexibility of tri-snRNP observed by classification

a, Different conformations of the Arm domain demonstrated by the unsharpened maps of the three major classes (purple, magenta and red) obtained from masked classification of the Arm domain alone followed by masked refinement with the Body and Arm domains. The Body domain was included in the refinement because the arm domain is too small for accurate alignments. b, The sharpened map of one of the three classes with Prp3 and LSm models shown. In the improved domain maps for the Arm domain, extra density for the N-terminal helix of Prp3 could be observed to extend to the LSm proteins. c, The sharpened map of the tri-snRNP and the locations of Snu66 and Prp8. d, The open and closed conformations of the Head and Foot domains of the tri-snRNP observed by global classification. The unsharpened maps for the two major classes obtained from global classification with finer angular sampling (1.8°) followed by 3D auto-refinement are shown. The open and closed states are indicated. e, Superposition of the unsharpened maps of the open (grey) and closed (yellow) states shown in d. The arrows indicate the rotations of the head and foot domains.

Extended Data Figure 7. Brr2 helicase and its U4/U6 snRNA substrate

a, domain structure of Brr2 helicase comprising the N-terminal domain and two helicase cassettes. Individual domains of N-terminal helicase cassette (NHC) are colour-coded. b, Extensive interactions of Brr2 with U4/U6 snRNA and Prp3. The single-stranded region of U4 snRNA extending from stem I enters the active site near the β-finger (red). c, 3′ stem of U4 snRNA interacts with the HLH domain of NHC. d, The N-terminal domain (NTD) of Brr2 interacts with a long helix of Prp3 and inserts a loop into U4/U6 Stem II. e, Snu66 has a long extended region that wraps around both helicase cassettes of Brr2.

Figure 1. Three orthogonal views of a near-complete atomic model of the Saccharomyces cerevisiae U4/U6.U5 tri-snRNP

Inset shows four subdomains.

Figure 2. Prp8 and U4/U6 and U5 snRNAs

a, Domain structure of Prp8: HB, helix bundle; RT, Reverse Transcriptase-like; Endo, Endonuclease-like; RH, RNaseH-like; JM, Jab1/MPN. b, Prp8 makes extensive interactions with U4/U6 and U5 snRNAs. c, The α-helix (residues 703-735) of the N-terminal domain fits into the minor groove of U5 snRNA and an extended polypeptide (residue 535-543) fits into the major groove on the opposite face, harnessing the RNA helix firmly in place. d, orthogonal view. U5 snRNA loop 1 interacts with the single-stranded region of U6 snRNA. e, The region around the ACAGAGA sequence forms a hairpin and is sandwiched between the Large and N-terminal domains of Prp8 and Dib1.

Figure 3. Snu114 and its interaction with Prp8 and U5 snRNA

a, Snu114, the N-terminal domain of Prp8 and U5 snRNA stems I and II form a stable domain in the Foot domain in U4/U6.U5 tri-snRNP. GTP is bound in the GTPase active site at the interface with the Prp8 N-terminal domain. b, Canonical interactions of GTP with surrounding residues in Snu114. c, The catalytic His218, hydrogen bonded to Tyr403 in Prp8, points away from the GTP γ-phosphate. d, Activation of EF-G GTPase upon binding to the sarcinricin (SR) loop in the ribosome. His87 moves closer to the γ-phosphate and places a water molecule.

Figure 4. Interactions of U4/U6 snRNAs with proteins

a, Overview of U4/U6 di-snRNP. b, the extraordinary structure of Prp3 and its multiple interactions with U4/U6 snRNA, Prp4, Snu13, the RNaseH-like domain of Prp8, Brr2 N-terminal domain and the LSm core domain. c, The C-terminal region of Prp31 extends along U4 snRNA 5′-stem towards the three-way junction. d, The C-terminal extension of Prp31 makes multiple interactions with U4/U6 snRNAs, Dib1, Prp8 α-finger and the N-terminal extension of Prp6. e, the Prp4 WD40 domain and Prp31 interact with the C-terminal TPR domain of Prp6.

Figure 5. B complex formation and activation mechanism

a, U4/U6.U5 tri-snRNP fits into the EM envelope of human complex B (reproduced from ref. 45 with permission), showing that U2 snRNP binds near the LSm core domain, Prp6 and Prp3. b, Overlay of the Prp8 large domain between tri-snRNP and the ILS shows how NTC/NTR might bind to complex B and interact with U2 snRNP so that U2 snRNP can be passed to the NTC/NTR complex. c, A comparison of the tri-snRNP and the ILS structures shows rotation of the Foot domain with respect to the Prp8 large domain. Upon rotation, Prp8 residues 602-614 will clash with Dib1 and ACAGAGA helix, causing them to dissociate thus liberating the ACAGAGA sequence to bind the 5′-splice site.