› 7a5p

Electron Microscopy
5Å resolution

Human C Complex Spliceosome - Medium-resolution PERIPHERY

Released:
DOI: 10.2210/pdb7a5p/pdb
PDB entry 7a5p coloured by chain, front view.
PDB entry 7a5p coloured by chain, side view.
PDB entry 7a5p coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Insights into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome.
Bertram K, El Ayoubi L, Dybkov O, Agafonov DE, Will CL, Hartmuth K, Urlaub H, Kastner B, Stark H, Lührmann R
Mol Cell 80 127-139.e6 (2020)
PMID: 33007253
Related structures: EMD-11570

Function and Biology Details

Reactions catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
ATP + H(2)O = ADP + phosphate
Peptidylproline (omega=180) = peptidylproline (omega=0)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 48-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-275954 (preferred)
Entry contents:
34 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (38 distinct):
UNKNOWN Chain: 8
Molecule details ›
Chain: 8
Length: 204 amino acids
Theoretical weight: 17.38 KDa
Source organism: Homo sapiens
Pre-mRNA-processing-splicing factor 8 Chain: A
Molecule details ›
Chain: A
Length: 2335 amino acids
Theoretical weight: 273.97 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6P2Q9 (Residues: 1-2335; Coverage: 100%)
Gene names: PRPC8, PRPF8
Sequence domains:
SNW domain-containing protein 1 Chain: C
Pre-mRNA-processing factor 17 Chain: E
Pre-mRNA-processing factor 19 Chains: G, H, I, J
Pre-mRNA-splicing factor SPF27 Chain: K
Cell division cycle 5-like protein Chain: L
Pre-mRNA-splicing factor SYF1 Chain: M
Pre-mRNA-splicing factor SYF2 Chain: N
Crooked neck-like protein 1 Chain: O
Pre-mRNA-splicing factor RBM22 Chain: P
Serine/arginine repetitive matrix protein 2 Chain: S
Pre-mRNA-splicing factor CWC22 homolog Chain: T
RNA helicase aquarius Chain: U
U2 small nuclear ribonucleoprotein A' Chain: W
U2 small nuclear ribonucleoprotein B'' Chain: X
Small nuclear ribonucleoprotein Sm D3 Chains: a, l
Small nuclear ribonucleoprotein-associated proteins B and B' Chains: b, m
Small nuclear ribonucleoprotein Sm D1 Chains: c, n
Small nuclear ribonucleoprotein Sm D2 Chains: d, h
Small nuclear ribonucleoprotein E Chains: e, j
Small nuclear ribonucleoprotein F Chains: f, i
Small nuclear ribonucleoprotein G Chains: g, k
Peptidyl-prolyl cis-trans isomerase E Chain: o
WD repeat-containing protein 70 Chain: p
U5 small nuclear ribonucleoprotein 200 kDa helicase Chain: q
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 Chain: r
Pre-mRNA-splicing factor ISY1 homolog Chain: s
Splicing factor YJU2 Chain: u
Protein mago nashi homolog Chain: v
RNA-binding protein 8A Chain: w
Protein FRG1 Chain: x
Eukaryotic initiation factor 4A-III Chain: y
Peptidylprolyl isomerase domain and WD repeat-containing protein 1 Chain: z
U2 snRNA Chain: 2
U5 snRNA Chain: 5
U6 snRNA Chain: 6
pre-mRNA Chain: Y

Ligands and Environments

No bound ligands
1 modified residue:
Ligand MSE 39 x MSE

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 5Å
Relevant EMDB volumes: EMD-11570

Quick links

Citations

5 review citations

Recent advances and current trends in cryo-electron microscopy.
Guaita et al. (2022)
4 more

2 mentions without citation

The debranching enzyme Dbr1 regulates lariat turnover and intron splicing.
Buerer et al. (2024)
1 more