PDBsum entry 5lj3

Splicing

PDB id: 5lj3

Contents

Protein chains

1922 a.a.

114 a.a.

46 a.a.

882 a.a.

97 a.a.

399 a.a.

326 a.a.

163 a.a.

155 a.a.

252 a.a.

209 a.a.

198 a.a.

36 a.a.

97 a.a.

464 a.a.

592 a.a.

80 a.a.

82 a.a.

75 a.a.

72 a.a.

69 a.a.

82 a.a.

94 a.a.

164 a.a.

84 a.a.

132 a.a.

DNA/RNA

Ligands

GTP

Metals

_MG ×2

_ZN ×7

PDB id:

5lj3

Name:

Splicing

Title:

Structure of the core of the yeast spliceosome immediately after branching

Structure:

U5 snrna (small nuclear RNA). Chain: u. Exon 1 (5' exon) of ubc4 pre-mRNA. Chain: e. Other_details: this RNA was produced from an in vitro transcribed yeast ubc4 pre-mRNA with two stem-loops added at the 5' end for binding by the ms2 bacteriophage coat protein. This pre-mRNA is added to a yeast splicing extract and the first step of splicing yields the 5' exon and the lariat intron-3' exon intermediate, which both remain

Source:

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

Authors:

W.P.Galej,M.F.Wilkinson,S.M.Fica,C.Oubridge,A.J.Newman,K.Nagai

Key ref:

W.P.Galej et al. (2016). Cryo-EM structure of the spliceosome immediately after branching. Nature, 537, 197-201. PubMed id: 27459055 DOI: 10.1038/nature19316

Date:

17-Jul-16 Release date: 03-Aug-16

Protein chain

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

Seq: 2413 a.a.

Struc: 1922 a.a.

Protein chain

P28320  (CWC16_YEAST) -  Splicing factor YJU2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 278 a.a.

Struc: 114 a.a.

Protein chain

P53854  (CWC25_YEAST) -  Pre-mRNA-splicing factor CWC25 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 179 a.a.

Struc: 46 a.a.

Protein chain

P36048  (SN114_YEAST) -  Pre-mRNA-splicing factor SNU114 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1008 a.a.

Struc: 882 a.a.

Protein chain

P21374  (ISY1_YEAST) -  Pre-mRNA-splicing factor ISY1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 235 a.a.

Struc: 97 a.a.

Protein chain

No UniProt id for this chain

Struc: 399 a.a.

Protein chain

Q12417  (PRP46_YEAST) -  Pre-mRNA-splicing factor PRP46 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 451 a.a.

Struc: 326 a.a.

Protein chain

P28004  (PRP45_YEAST) -  Pre-mRNA-processing protein 45 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 379 a.a.

Struc: 163 a.a.

Protein chain

P25337  (BUD31_YEAST) -  Pre-mRNA-splicing factor BUD31 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 157 a.a.

Struc: 155 a.a.

Protein chain

Q12046  (CWC2_YEAST) -  Pre-mRNA-splicing factor CWC2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 339 a.a.

Struc: 252 a.a.*

Protein chain

P38241  (SLT11_YEAST) -  Pre-mRNA-splicing factor SLT11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 364 a.a.

Struc: 209 a.a.

Protein chain

Q03654  (CEF1_YEAST) -  Pre-mRNA-splicing factor CEF1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 590 a.a.

Struc: 198 a.a.

Protein chain

Q03772  (CWC15_YEAST) -  Pre-mRNA-splicing factor CWC15 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 175 a.a.

Struc: 36 a.a.

Protein chain

Q03375  (CWC21_YEAST) -  Pre-mRNA-splicing factor CWC21 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 135 a.a.

Struc: 97 a.a.

Protein chain

Q12309  (CLF1_YEAST) -  Pre-mRNA-splicing factor CLF1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 687 a.a.

Struc: 464 a.a.*

Protein chain

Q04048  (SYF1_YEAST) -  Pre-mRNA-splicing factor SYF1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 859 a.a.

Struc: 592 a.a.*

Protein chains

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 chains

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

Seq: 101 a.a.

Struc: 82 a.a.

Protein chains

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

Seq: 94 a.a.

Struc: 75 a.a.

Protein chains

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

Seq: 86 a.a.

Struc: 72 a.a.

Protein chains

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

Seq: 77 a.a.

Struc: 69 a.a.

Protein chains

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

Seq: 146 a.a.

Struc: 82 a.a.

Protein chains

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

Q08963  (RU2A_YEAST) -  U2 small nuclear ribonucleoprotein A' from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 238 a.a.

Struc: 164 a.a.

Protein chain

P40567  (MSL1_YEAST) -  U2 small nuclear ribonucleoprotein B'' from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 111 a.a.

Struc: 84 a.a.

Protein chain

No UniProt id for this chain

Struc: 132 a.a.

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DNA/RNA chains

C-A-G-C-U-U-U-A-C-A-G-A-U-C-A-A-U-G-G-C-G-G-A-G-G-G-A-G-G-U-C-A-A-C-A-U-C-A-A- 141 bases

U-A-A-G-U-G-A-U-C-U-A-G-A-A-A-G 16 bases

G-U-A-U-G-U-C-U-A-A-A-U-G-C-U-C-U-U-A-U-U-U-A-C-U-A-A-C-A-A-A-A-U 33 bases

G-A-A-U-C-U-C-U-U-U-G-C-C-U-U-U-U-G-G-C-U-U-A-G-A-U-C-A-A-G-U-G-U-A-G-U-A-U-C- 171 bases

G-U-U-C-G-C-G-A-A-G-C-U-U-C-G-U-G-G-A-C-A-U-U-U-G-G-U-C-A-A-U-U-U-G-A-A-A-C-A- 97 bases

DOI no: 10.1038/nature19316

Nature 537:197-201 (2016)

PubMed id: 27459055

Cryo-EM structure of the spliceosome immediately after branching.

W.P.Galej, M.E.Wilkinson, S.M.Fica, C.Oubridge, A.J.Newman, K.Nagai.

ABSTRACT

No abstract given.