PDBsum entry 5gao

Transcription

PDB id: 5gao

Contents

Protein chains

80 a.a.

91 a.a.

94 a.a.

82 a.a.

76 a.a.

72 a.a.

69 a.a.

338 a.a.

1710 a.a.

255 a.a.

DNA/RNA

PDB id:

5gao

Name:

Transcription

Title:

Head region of the yeast spliceosomal u4/u6.U5 tri-snrnp

Structure:

Small nuclear ribonucleoprotein-associated protein b. Chain: k. Synonym: snrnp-b,sm protein b,smb. Other_details: the smb protein from the u4 snrnp sm protein ring. ThE C-terminus is disordered in this and other previously reported structures.. Small nuclear ribonucleoprotein sm d1. Chain: l. Synonym: sm-d1,snrnp core protein d1.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: bcy123. Strain: bcy123

Authors:

T.H.D.Nguyen,W.P.Galej,X.C.Bai,C.Oubridge,S.H.W.Scheres,A.J.Newman, K.Nagai

Key ref:

T.H.Nguyen et al. (2016). Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution. Nature, 530, 298-302. PubMed id: 26829225 DOI: 10.1038/nature16940

Date:

15-Dec-15 Release date: 27-Jan-16

Protein chain

P40018  (RSMB_YEAST) -  Small nuclear ribonucleoprotein-associated protein B from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 196 a.a.

Struc: 80 a.a.

Protein chain

Q02260  (SMD1_YEAST) -  Small nuclear ribonucleoprotein Sm D1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 146 a.a.

Struc: 91 a.a.

Protein chain

Q06217  (SMD2_YEAST) -  Small nuclear ribonucleoprotein Sm D2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 110 a.a.

Struc: 94 a.a.

Protein chain

P43321  (SMD3_YEAST) -  Small nuclear ribonucleoprotein Sm D3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 101 a.a.

Struc: 82 a.a.

Protein chain

Q12330  (RUXE_YEAST) -  Small nuclear ribonucleoprotein E from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 94 a.a.

Struc: 76 a.a.

Protein chain

P54999  (RUXF_YEAST) -  Small nuclear ribonucleoprotein F from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 86 a.a.

Struc: 72 a.a.

Protein chain

P40204  (RUXG_YEAST) -  Small nuclear ribonucleoprotein G from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 77 a.a.

Struc: 69 a.a.

Protein chain

Q12420  (SNU66_YEAST) -  66 kDa U4/U6.U5 small nuclear ribonucleoprotein component from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Protein chain

P32639  (BRR2_YEAST) -  Pre-mRNA-splicing helicase BRR2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 2163 a.a.

Struc: 1710 a.a.

Protein chain

P33334  (PRP8_YEAST) -  Pre-mRNA-splicing factor 8 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 2413 a.a.

Struc: 255 a.a.

DNA/RNA chain

A-U-U-A-U-A-A-A-C-C-A-G-A-C-C-G-U-C-U-C-C-U-C-A-U-G-G-U-C-A-A-U-C-A-A-G-A-C-U- 57 bases

Enzyme reactions

• Enzyme class: Chain B: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nature16940

Nature 530:298-302 (2016)

PubMed id: 26829225

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

T.H.Nguyen, W.P.Galej, X.C.Bai, C.Oubridge, A.J.Newman, S.H.Scheres, K.Nagai.

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.