PDBsum entry 5lj5

Splicing

PDB id: 5lj5

Contents

Protein chains

2168 a.a.

1707 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.

283 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.

619 a.a.

438 a.a.

110 a.a.

132 a.a.

DNA/RNA

Ligands

GTP

Metals

_MG ×2

_ZN ×7

PDB id:

5lj5

Name:

Splicing

Title:

Overall structure 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. Intron of ubc4 pre-mRNA. Chain: i. U2 snrna (small nuclear RNA). Chain: z. U6 snrna (small nuclear RNA).

Source:

Saccharomyces cerevisiae. Organism_taxid: 4932. 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: 31-Aug-16

Protein chain

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

Seq: 2413 a.a.

Struc: 2168 a.a.

Protein chain

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

Seq: 2163 a.a.

Struc: 1707 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: 283 a.a.

Protein chain

No UniProt id for this chain

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

P15938  (PRP16_YEAST) -  Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1071 a.a.

Struc: 619 a.a.

Protein chains

P32523  (PRP19_YEAST) -  Pre-mRNA-processing factor 19 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 503 a.a.

Struc: 438 a.a.

Protein chain

Q06091  (SN309_YEAST) -  Pre-mRNA-splicing factor SNT309 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 175 a.a.

Struc: 110 a.a.

Protein chain

No UniProt id for this chain

Struc: 132 a.a.

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

Enzyme reactions

• Enzyme class 2: Chains B, Q: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP (Bound ligand (Het Group name = GTP) matches with 96.88% similarity) + H2O = ADP + phosphate + H(+)

• Enzyme class 3: Chains t, u, v, w: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

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.