PDBsum entry 3jb9

RNA binding protein/RNA

PDB id: 3jb9

Contents

Protein chains

1964 a.a.

904 a.a.

96 a.a.

98 a.a.

82 a.a.

95 a.a.

76 a.a.

73 a.a.

73 a.a.

373 a.a.

293 a.a.

207 a.a.

132 a.a.

430 a.a.

426 a.a.

261 a.a.

255 a.a.

300 a.a.

155 a.a.

144 a.a.

148 a.a.

90 a.a.

161 a.a.

575 a.a.

573 a.a.

1195 a.a.

160 a.a.

89 a.a.

80 a.a.

74 a.a.

87 a.a.

DNA/RNA

Ligands

GDP

ADP

Metals

_MG ×4

_ZN ×7

PDB id:

3jb9

Name:

RNA binding protein/RNA

Title:

Cryo-em structure of the yeast spliceosome at 3.6 angstrom resolution

Structure:

Pre-mRNA-splicing factor spp42. Chain: a. Synonym: complexed with cdc5 protein 6. Pre-mRNA-splicing factor cwf10. Chain: b. Synonym: 114 kda u5 small nuclear ribonucleoprotein component homolog, complexed with cdc5 protein 10. U5 snrna. Chain: c.

Source:

Schizosaccharomyces pombe 972h-. Fission yeast. Organism_taxid: 284812. Strain: 972 / atcc 24843. Schizosaccharomyces pombe. Organism_taxid: 4896. Strain: 972 / atcc 24843

Authors:

C.Yan,J.Hang,R.Wan,M.Huang,C.Wong,Y.Shi

Key ref:

C.Yan et al. (2015). Structure of a yeast spliceosome at 3.6-angstrom resolution. Science, 349, 1182-1191. PubMed id: 26292707 DOI: 10.1126/science.aac7629

Date:

09-Aug-15 Release date: 23-Sep-15

Protein chain

O14187  (SPP42_SCHPO) -  Pre-mRNA-splicing factor spp42 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 2363 a.a.

Struc: 1964 a.a.

Protein chain

O94316  (SN114_SCHPO) -  Pre-mRNA-splicing factor cwf10 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 984 a.a.

Struc: 904 a.a.

Protein chain

Q9UUC6  (SMD3_SCHPO) -  Small nuclear ribonucleoprotein Sm D3 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 97 a.a.

Struc: 96 a.a.

Protein chain

Q10163  (RSMB_SCHPO) -  Small nuclear ribonucleoprotein-associated protein B from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 147 a.a.

Struc: 98 a.a.

Protein chains

O42661  (SMD1_SCHPO) -  Small nuclear ribonucleoprotein Sm D1 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 117 a.a.

Struc: 82 a.a.

Protein chain

O14036  (SMD2_SCHPO) -  Small nuclear ribonucleoprotein Sm D2 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 115 a.a.

Struc: 95 a.a.

Protein chains

Q9USZ3  (RUXE_SCHPO) -  Small nuclear ribonucleoprotein E from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 84 a.a.

Struc: 76 a.a.

Protein chains

O59734  (RUXF_SCHPO) -  Small nuclear ribonucleoprotein F from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 78 a.a.

Struc: 73 a.a.*

Protein chains

O74966  (RUXG_SCHPO) -  Small nuclear ribonucleoprotein G from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 77 a.a.

Struc: 73 a.a.

Protein chain

O13615  (PRP46_SCHPO) -  Pre-mRNA-splicing factor prp5 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 473 a.a.

Struc: 373 a.a.*

Protein chain

O94620  (CWF17_SCHPO) -  Pre-mRNA-splicing factor cwf17 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 340 a.a.

Struc: 293 a.a.

Protein chain

Q09882  (PRP45_SCHPO) -  Pre-mRNA-processing protein 45 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 557 a.a.

Struc: 207 a.a.

Protein chains

O14011  (PRP19_SCHPO) -  Pre-mRNA-processing factor 19 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 488 a.a.

Struc: 132 a.a.

Protein chain

O14011  (PRP19_SCHPO) -  Pre-mRNA-processing factor 19 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 488 a.a.

Struc: 430 a.a.

Protein chain

P39964  (CEF1_SCHPO) -  Pre-mRNA-splicing factor cdc5 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 757 a.a.

Struc: 426 a.a.*

Protein chains

P87126  (CWC2_SCHPO) -  Pre-mRNA-splicing factor cwf2 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 388 a.a.

Struc: 261 a.a.*

Protein chain

O59800  (SLT11_SCHPO) -  Pre-mRNA-splicing factor cwf5 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 354 a.a.

Struc: 255 a.a.*

Protein chain

Q09909  (CWF19_SCHPO) -  Pre-mRNA-splicing factor cwf19 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 639 a.a.

Struc: 300 a.a.

Protein chain

P87051  (PPIL1_SCHPO) -  Peptidyl-prolyl cis-trans isomerase ppi1 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 155 a.a.

Struc: 155 a.a.

Protein chain

O74772  (CWF14_SCHPO) -  Pre-mRNA-splicing factor cwf14 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 146 a.a.

Struc: 144 a.a.

Protein chain

O43071  (PRP17_SCHPO) -  Pre-mRNA-processing factor 17 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 558 a.a.

Struc: 148 a.a.

Protein chain

P78794  (CWC15_SCHPO) -  Pre-mRNA-splicing factor cwf15 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 265 a.a.

Struc: 90 a.a.*

Protein chain

Q9USV3  (SPF27_SCHPO) -  Pre-mRNA-splicing factor cwf7 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 187 a.a.

Struc: 161 a.a.

Protein chain

P87312  (CLF1_SCHPO) -  Pre-mRNA-splicing factor cwf4 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 674 a.a.

Struc: 575 a.a.*

Protein chain

Q9P7R9  (SYF1_SCHPO) -  Pre-mRNA-splicing factor cwf3 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 790 a.a.

Struc: 573 a.a.*

Protein chain

O94508  (CWF11_SCHPO) -  Pre-mRNA-splicing factor cwf11 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 1284 a.a.

Struc: 1195 a.a.

Protein chain

Q9USX8  (RU2A_SCHPO) -  U2 small nuclear ribonucleoprotein A' from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 239 a.a.

Struc: 160 a.a.

Protein chain

Q7LL14  (RU2B_SCHPO) -  Probable U2 small nuclear ribonucleoprotein B'' from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 111 a.a.

Struc: 89 a.a.

Protein chain

Q9UUC6  (SMD3_SCHPO) -  Small nuclear ribonucleoprotein Sm D3 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 97 a.a.

Struc: 80 a.a.

Protein chain

Q10163  (RSMB_SCHPO) -  Small nuclear ribonucleoprotein-associated protein B from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 147 a.a.

Struc: 74 a.a.

Protein chain

O14036  (SMD2_SCHPO) -  Small nuclear ribonucleoprotein Sm D2 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 115 a.a.

Struc: 87 a.a.

* PDB and UniProt seqs differ at 1188 residue positions (black crosses)

DNA/RNA chains

C-G-U-C-A-A-A-G-C-A-C-U-U-U-G-C-A-A-A-A-G-C-U-A-A-C-G-U-A-U-C-U-G-U-U-U-C-U-U- 105 bases

G-A-U-C-U-U-C-G-G-A-U-C-A-C-U-U-U-G-G-U-C-A-A-A-U-U-G-A-A-A-C-G-A-U-A-C-A-G-A- 90 bases

G-U-A-U-G-U-A-U 8 bases

U-U-U-A-U-A-C-U-A-A-C-A-C 13 bases

A-U-U-C-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- 111 bases

Enzyme reactions

• Enzyme class 2: Chain d: E.C.5.2.1.8 - peptidylprolyl isomerase.
• Reaction: [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0)
• Enzyme class 3: Chains S, T, U, V: 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

Added reference

DOI no: 10.1126/science.aac7629

Science 349:1182-1191 (2015)

PubMed id: 26292707

Structure of a yeast spliceosome at 3.6-angstrom resolution.

C.Yan, J.Hang, R.Wan, M.Huang, C.C.Wong, Y.Shi.

ABSTRACT

Splicing of precursor messenger RNA (pre-mRNA) in yeast is executed by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs), NTC (nineteen complex), NTC-related proteins (NTR), and a number of associated enzymes and cofactors. Here, we report the three-dimensional structure of a Schizosaccharomyces pombe spliceosome at 3.6-angstrom resolution, revealed by means of single-particle cryogenic electron microscopy. This spliceosome contains U2 and U5 snRNPs, NTC, NTR, U6 small nuclear RNA, and an RNA intron lariat. The atomic model includes 10,574 amino acids from 37 proteins and four RNA molecules, with a combined molecular mass of approximately 1.3 megadaltons. Spp42 (Prp8 in Saccharomyces cerevisiae), the key protein component of the U5 snRNP, forms a central scaffold and anchors the catalytic center. Both the morphology and the placement of protein components appear to have evolved to facilitate the dynamic process of pre-mRNA splicing. Our near-atomic-resolution structure of a central spliceosome provides a molecular framework for mechanistic understanding of pre-mRNA splicing.