PDBsum entry 6id1

Splicing

PDB id: 6id1

Contents

Protein chains

1981 a.a.

888 a.a.

303 a.a.

568 a.a.

475 a.a.

130 a.a.

143 a.a.

290 a.a.

118 a.a.

272 a.a.

159 a.a.

317 a.a.

158 a.a.

347 a.a.

81 a.a.

86 a.a.

82 a.a.

97 a.a.

74 a.a.

79 a.a.

74 a.a.

132 a.a.

67 a.a.

152 a.a.

576 a.a.

1322 a.a.

79 a.a.

85 a.a.

67 a.a.

162 a.a.

94 a.a.

663 a.a.

DNA/RNA

Ligands

IHP

GTP

Metals

_MG ×7

_ZN ×7

PDB id:

6id1

Name:

Splicing

Title:

Cryo-em structure of a human intron lariat spliceosome after prp43 loaded (ils2 complex) at 2.9 angstrom resolution

Structure:

Pre-mRNA-processing-splicing factor 8. Chain: a. Synonym: 220 kda u5 snrnp-specific protein,prp8 homolog,splicing factor prp8,p220. U5snrna. Chain: b. 116 kda u5 small nuclear ribonucleoprotein component. Chain: c. Synonym: elongation factor tu gtp-binding domain-containing protein

Source:

Homo sapiens. Human. Organism_taxid: 9606. Organism_taxid: 9606

Authors:

X.Zhang,X.Zhan,C.Yan,Y.Shi

Key ref:

X.Zhang et al. (2019). Structures of the human spliceosomes before and after release of the ligated exon. Cell Res, 29, 274-285. PubMed id: 30728453 DOI: 10.1038/s41422-019-0143-x

Date:

07-Sep-18 Release date: 13-Mar-19

Protein chain

Q6P2Q9  (PRP8_HUMAN) -  Pre-mRNA-processing-splicing factor 8 from Homo sapiens

Seq: 2335 a.a.

Struc: 1981 a.a.

Protein chain

Q15029  (U5S1_HUMAN) -  116 kDa U5 small nuclear ribonucleoprotein component from Homo sapiens

Seq: 972 a.a.

Struc: 888 a.a.

Protein chain

Q96DI7  (SNR40_HUMAN) -  U5 small nuclear ribonucleoprotein 40 kDa protein from Homo sapiens

Seq: 357 a.a.

Struc: 303 a.a.

Protein chain

Q9BZJ0  (CRNL1_HUMAN) -  Crooked neck-like protein 1 from Homo sapiens

Seq: 848 a.a.

Struc: 568 a.a.

Protein chain

Q99459  (CDC5L_HUMAN) -  Cell division cycle 5-like protein from Homo sapiens

Seq: 802 a.a.

Struc: 475 a.a.

Protein chain

O95926  (SYF2_HUMAN) -  Pre-mRNA-splicing factor SYF2 from Homo sapiens

Seq: 243 a.a.

Struc: 130 a.a.

Protein chain

P41223  (BUD31_HUMAN) -  Protein BUD31 homolog from Homo sapiens

Seq: 144 a.a.

Struc: 143 a.a.

Protein chain

Q9NW64  (RBM22_HUMAN) -  Pre-mRNA-splicing factor RBM22 from Homo sapiens

Seq: 420 a.a.

Struc: 290 a.a.

Protein chain

Q9P013  (CWC15_HUMAN) -  Spliceosome-associated protein CWC15 homolog from Homo sapiens

Seq: 229 a.a.

Struc: 118 a.a.

Protein chain

Q13573  (SNW1_HUMAN) -  SNW domain-containing protein 1 from Homo sapiens

Seq: 536 a.a.

Struc: 272 a.a.

Protein chain

Q9Y3C6  (PPIL1_HUMAN) -  Peptidyl-prolyl cis-trans isomerase-like 1 from Homo sapiens

Seq: 166 a.a.

Struc: 159 a.a.

Protein chain

O43660  (PLRG1_HUMAN) -  Pleiotropic regulator 1 from Homo sapiens

Seq: 514 a.a.

Struc: 317 a.a.

Protein chain

O60508  (PRP17_HUMAN) -  Pre-mRNA-processing factor 17 from Homo sapiens

Seq: 579 a.a.

Struc: 158 a.a.

Protein chain

Q2TBE0  (C19L2_HUMAN) -  CWF19-like protein 2 from Homo sapiens

Seq: 894 a.a.

Struc: 347 a.a.

Protein chains

P62318  (SMD3_HUMAN) -  Small nuclear ribonucleoprotein Sm D3 from Homo sapiens

Seq: 126 a.a.

Struc: 81 a.a.

Protein chains

P14678  (RSMB_HUMAN) -  Small nuclear ribonucleoprotein-associated proteins B and B' from Homo sapiens

Seq: 240 a.a.

Struc: 86 a.a.

Protein chains

P62314  (SMD1_HUMAN) -  Small nuclear ribonucleoprotein Sm D1 from Homo sapiens

Seq: 119 a.a.

Struc: 82 a.a.

Protein chain

P62316  (SMD2_HUMAN) -  Small nuclear ribonucleoprotein Sm D2 from Homo sapiens

Seq: 118 a.a.

Struc: 97 a.a.

Protein chains

P62306  (RUXF_HUMAN) -  Small nuclear ribonucleoprotein F from Homo sapiens

Seq: 86 a.a.

Struc: 74 a.a.

Protein chains

P62304  (RUXE_HUMAN) -  Small nuclear ribonucleoprotein E from Homo sapiens

Seq: 92 a.a.

Struc: 79 a.a.

Protein chain

P62308  (RUXG_HUMAN) -  Small nuclear ribonucleoprotein G from Homo sapiens

Seq: 76 a.a.

Struc: 74 a.a.

Protein chains

Q9UMS4  (PRP19_HUMAN) -  Pre-mRNA-processing factor 19 from Homo sapiens

Seq: 504 a.a.

Struc: 132 a.a.

Protein chains

Q9UMS4  (PRP19_HUMAN) -  Pre-mRNA-processing factor 19 from Homo sapiens

Seq: 504 a.a.

Struc: 67 a.a.

Protein chain

O75934  (SPF27_HUMAN) -  Pre-mRNA-splicing factor SPF27 from Homo sapiens

Seq: 225 a.a.

Struc: 152 a.a.

Protein chain

Q9HCS7  (SYF1_HUMAN) -  Pre-mRNA-splicing factor SYF1 from Homo sapiens

Seq: 855 a.a.

Struc: 576 a.a.

Protein chain

O60306  (AQR_HUMAN) -  RNA helicase aquarius from Homo sapiens

Seq: 1485 a.a.

Struc: 1322 a.a.

Protein chain

Q9UNP9  (PPIE_HUMAN) -  Peptidyl-prolyl cis-trans isomerase E from Homo sapiens

Seq: 301 a.a.

Struc: 79 a.a.

Protein chain

P62316  (SMD2_HUMAN) -  Small nuclear ribonucleoprotein Sm D2 from Homo sapiens

Seq: 118 a.a.

Struc: 85 a.a.

Protein chain

P62308  (RUXG_HUMAN) -  Small nuclear ribonucleoprotein G from Homo sapiens

Seq: 76 a.a.

Struc: 67 a.a.

Protein chain

P09661  (RU2A_HUMAN) -  U2 small nuclear ribonucleoprotein A' from Homo sapiens

Seq: 255 a.a.

Struc: 162 a.a.

Protein chain

P08579  (RU2B_HUMAN) -  U2 small nuclear ribonucleoprotein B'' from Homo sapiens

Seq: 225 a.a.

Struc: 94 a.a.

Protein chain

O43143  (DHX15_HUMAN) -  ATP-dependent RNA helicase DHX15 from Homo sapiens

Seq: 795 a.a.

Struc: 663 a.a.

DNA/RNA chains

U-G-G-U-U-U-C-U-C-U-U-C-A-G-A-U-C-G-C-A-U-A-A-A-U-C-U-U-U-C-G-C-C-U-U-U-U-A-C- 98 bases

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

G-U-A-A-G-A-G-C-C-U-A-G-C-A-U-G-U-A-G-A-A-C-U-G-G-U-U-A-C-C-A-G-G-G-U-U-U-C-C- 68 bases

A-U-C-G-C-U-U-C-U-C-G-G-C-C-U-U-U-U-G-G-C-U-A-A-G-A-U-C-A-A-G-U-G-U-A-G-U-A-U- 136 bases

Enzyme reactions

• Enzyme class 1: Chains Q, V: 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 2: Chains q, r, s, t: 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
• Enzyme class 3: Chains S, y: E.C.5.2.1.8 - peptidylprolyl isomerase.
• Reaction: [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0)

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/s41422-019-0143-x

Cell Res 29:274-285 (2019)

PubMed id: 30728453

Structures of the human spliceosomes before and after release of the ligated exon.

X.Zhang, X.Zhan, C.Yan, W.Zhang, D.Liu, J.Lei, Y.Shi.

ABSTRACT

Pre-mRNA splicing is executed by the spliceosome, which has eight major functional states each with distinct composition. Five of these eight human spliceosomal complexes, all preceding exon ligation, have been structurally characterized. In this study, we report the cryo-electron microscopy structures of the human post-catalytic spliceosome (P complex) and intron lariat spliceosome (ILS) at average resolutions of 3.0 and 2.9 Å, respectively. In the P complex, the ligated exon remains anchored to loop I of U5 small nuclear RNA, and the 3'-splice site is recognized by the junction between the 5'-splice site and the branch point sequence. The ATPase/helicase Prp22, along with the ligated exon and eight other proteins, are dissociated in the P-to-ILS transition. Intriguingly, the ILS complex exists in two distinct conformations, one with the ATPase/helicase Prp43 and one without. Comparison of these three late-stage human spliceosomes reveals mechanistic insights into exon release and spliceosome disassembly.