5Y88: Cryo-EM structure of the intron-lariat spliceosome ready for disassembly from S.cerevisiae at 3.5 angstrom

PDB ID: 5Y88Download
MMDB ID: 164846
PDB Deposition Date: 2017/8/20
Updated in MMDB: 2022/11
Experimental Method:
electron microscopy
Resolution: 3.46  Å
Source Organism:
Similar Structures:
Biological Unit for 5Y88: 44-meric; determined by author
Molecular Components in 5Y88
Label Count Molecule
Proteins (39 molecules)
1
Pre-mrna-splicing Factor 8
(Gene symbol: PRP8)
Molecule annotation
1
Pre-mrna-splicing Factor Snu114
(Gene symbol: SNU114)
Molecule annotation
1
Pre-mrna-splicing Factor Snt309
(Gene symbol: SNT309)
Molecule annotation
1
Pre-mrna-splicing Factor Syf1
(Gene symbol: SYF1)
Molecule annotation
1
Pre-mrna-splicing Factor Clf1
(Gene symbol: CLF1)
Molecule annotation
1
Pre-mrna-splicing Factor Cef1
(Gene symbol: CEF1)
Molecule annotation
1
Pre-mrna-splicing Factor Syf2
(Gene symbol: SYF2)
Molecule annotation
1
Pre-mrna-splicing Factor Bud31
(Gene symbol: BUD31)
Molecule annotation
1
Pre-mrna-splicing Factor Slt11
(Gene symbol: ECM2)
Molecule annotation
1
Pre-mrna-splicing Factor Cwc2
(Gene symbol: CWC2)
Molecule annotation
1
Pre-mrna-splicing Factor Prp46
(Gene symbol: PRP46)
Molecule annotation
1
Pre-mrna-splicing Factor Cwc15
(Gene symbol: CWC15)
Molecule annotation
1
Pre-mrna-processing Protein 45
(Gene symbol: PRP45)
Molecule annotation
1
Protein Cwc16
(Gene symbol: YJU2)
Molecule annotation
1
Pre-mrna-processing Factor 17
(Gene symbol: CDC40)
Molecule annotation
1
Pre-mrna-splicing Factor Cwc23
(Gene symbol: CWC23)
Molecule annotation
1
Pre-mrna-splicing Factor Spp382
(Gene symbol: SPP382)
Molecule annotation
1
Pre-mrna-splicing Factor Ntr2
(Gene symbol: NTR2)
Molecule annotation
1
Pre-mrna-splicing Factor Atp-dependent RNA Helicase Prp43
(Gene symbol: PRP43)
Molecule annotation
2
Small Nuclear Ribonucleoprotein-associated Protein B
(Gene symbol: SMB1)
Molecule annotation
2
Small Nuclear Ribonucleoprotein E
(Gene symbol: SME1)
Molecule annotation
2
Small Nuclear Ribonucleoprotein F
(Gene symbol: SMX3)
Molecule annotation
2
Small Nuclear Ribonucleoprotein G
(Gene symbol: SMX2)
Molecule annotation
2
Small Nuclear Ribonucleoprotein SM D3
(Gene symbol: SMD3)
Molecule annotation
2
Small Nuclear Ribonucleoprotein SM D1
(Gene symbol: SMD1)
Molecule annotation
2
Small Nuclear Ribonucleoprotein SM D2
(Gene symbol: SMD2)
Molecule annotation
1
U2 Small Nuclear Ribonucleoprotein A'
(Gene symbol: LEA1)
Molecule annotation
1
U2 Small Nuclear Ribonucleoprotein B''
(Gene symbol: MSL1)
Molecule annotation
4
Pre-mrna-processing Factor 19
(Gene symbol: PRP19)
Molecule annotation
Nucleotides(5 molecules)
1
U5 Snrna
Molecule annotation
1
U6 Snrna
Molecule annotation
1
Intron Lariat
Molecule annotation
1
U2 Snrna
Molecule annotation
1
RNA (Intron or U6 Snrna)
Molecule annotation
Chemicals and Non-standard biopolymers (14 molecules)
1
1
INOSITOL HEXAKISPHOSPHATEINOSITOL HEXAKISPHOSPHATE
2
1
GUANOSINE-5'-TRIPHOSPHATEGUANOSINE-5'-TRIPHOSPHATE
3
6
MAGNESIUM IONMAGNESIUM ION
4
6
ZINC IONZINC ION
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303