5XJC: Cryo-EM structure of the human spliceosome just prior to exon ligation at 3.6 angstrom

PDB ID: 5XJCDownload
MMDB ID: 171429
PDB Deposition Date: 2017/4/30
Updated in MMDB: 2022/11
Experimental Method:
electron microscopy
Resolution: 3.6  Å
Source Organism:
Similar Structures:
Biological Unit for 5XJC: 50-meric; determined by author
Molecular Components in 5XJC
Label Count Molecule
Proteins (46 molecules)
1
Pre-mrna-processing-splicing Factor 8
Molecule annotation
1
116 KDA U5 Small Nuclear Ribonucleoprotein Component
Molecule annotation
1
U5 Small Nuclear Ribonucleoprotein 200 KDA Helicase
Molecule annotation
1
U5 Small Nuclear Ribonucleoprotein 40 KDA Protein
Molecule annotation
1
Pre-mrna-splicing Factor Syf1
Molecule annotation
1
Crooked Neck-like Protein 1
Molecule annotation
1
Pre-mrna-splicing Factor Spf27
Molecule annotation
1
Cell Division Cycle 5-like Protein
Molecule annotation
1
Pre-mrna-splicing Factor Syf2
Molecule annotation
1
Protein Bud31 Homolog
Molecule annotation
1
Pre-mrna-splicing Factor Rbm22
Molecule annotation
1
Spliceosome-associated Protein Cwc15 Homolog
Molecule annotation
1
Intron-binding Protein Aquarius
Molecule annotation
1
SNW Domain-containing Protein 1
Molecule annotation
1
Peptidyl-prolyl Cis-trans Isomerase-like 1
Molecule annotation
1
Pleiotropic Regulator 1
Molecule annotation
1
Serine/arginine Repetitive Matrix Protein 2
Molecule annotation
1
Pre-mrna-splicing Factor Cwc22 Homolog
Molecule annotation
1
Pre-mrna-processing Factor 17
Molecule annotation
1
Prkr-interacting Protein 1
Molecule annotation
1
Atp-dependent RNA Helicase Dhx8
Molecule annotation
1
Pre-mrna-splicing Factor Slu7
Molecule annotation
2
Small Nuclear Ribonucleoprotein SM D3
Molecule annotation
2
Small Nuclear Ribonucleoprotein-associated Proteins B and B'
Molecule annotation
2
Small Nuclear Ribonucleoprotein SM D1
Molecule annotation
2
Small Nuclear Ribonucleoprotein SM D2
Molecule annotation
2
Small Nuclear Ribonucleoprotein F
Molecule annotation
2
Small Nuclear Ribonucleoprotein E
Molecule annotation
2
Small Nuclear Ribonucleoprotein G
Molecule annotation
1
U2 Small Nuclear Ribonucleoprotein A'
Molecule annotation
1
U2 Small Nuclear Ribonucleoprotein B''
Molecule annotation
4
Pre-mrna-processing Factor 19
Molecule annotation
1
Eukaryotic Initiation Factor 4a-iii
Molecule annotation
1
Protein Mago Nashi Homolog 2
Molecule annotation
1
RNA-binding Protein 8A
Molecule annotation
1
Protein Casc3
Molecule annotation
Nucleotides(3 molecules)
1
U5 Snrna
Molecule annotation
1
U6 Snrna
Molecule annotation
1
Homo Sapiens Small Nuclear RNA (U2) Gene
Molecule annotation
Chemicals and Non-standard biopolymers (25 molecules)
G
1
pre-mRNA
1
1
INOSITOL HEXAKISPHOSPHATE (Link to PubChem not yet available)INOSITOL HEXAKISPHOSPHATE
2
1
GUANOSINE-5'-TRIPHOSPHATE (Link to PubChem not yet available)GUANOSINE-5'-TRIPHOSPHATE
3
11
MAGNESIUM ION (Link to PubChem not yet available)MAGNESIUM ION
4
2
ADENOSINE-5'-DIPHOSPHATE (Link to PubChem not yet available)ADENOSINE-5'-DIPHOSPHATE
5
7
ZINC ION (Link to PubChem not yet available)ZINC ION
6
2
ADENOSINE-5'-TRIPHOSPHATE (Link to PubChem not yet available)ADENOSINE-5'-TRIPHOSPHATE
* 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