› 7aav

Electron Microscopy
4.2Å resolution

Human pre-Bact-2 spliceosome core structure

Released:
DOI: 10.2210/pdb7aav/pdb
PDB entry 7aav coloured by chain, front view.
PDB entry 7aav coloured by chain, side view.
PDB entry 7aav coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation.
Townsend C, Leelaram MN, Agafonov DE, Dybkov O, Will CL, Bertram K, Urlaub H, Kastner B, Stark H, Lührmann R
Science 370 (2020)
PMID: 33243851
Related structures: EMD-11693

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero heptadecamer (preferred)
PDBe Complex ID:
PDB-CPX-129052 (preferred)
Entry contents:
13 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (17 distinct):
116 kDa U5 small nuclear ribonucleoprotein component Chain: r
Molecule details ›
Chain: r
Length: 972 amino acids
Theoretical weight: 109.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15029 (Residues: 1-972; Coverage: 100%)
Gene names: EFTUD2, KIAA0031, SNRP116
Sequence domains:
Protein BUD31 homolog Chain: Q
Molecule details ›
Chain: Q
Length: 144 amino acids
Theoretical weight: 17.03 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P41223 (Residues: 1-144; Coverage: 100%)
Gene names: BUD31, EDG2
Sequence domains: Pre-mRNA-splicing factor BUD31
Cell division cycle 5-like protein Chain: L
Molecule details ›
Chain: L
Length: 802 amino acids
Theoretical weight: 92.41 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q99459 (Residues: 1-802; Coverage: 100%)
Gene names: CDC5L, KIAA0432, PCDC5RP
Sequence domains:
Spliceosome-associated protein CWC15 homolog Chain: R
Molecule details ›
Chain: R
Length: 229 amino acids
Theoretical weight: 26.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9P013 (Residues: 1-229; Coverage: 100%)
Gene names: AD-002, C11orf5, CWC15, HSPC148
Sequence domains: Cwf15/Cwc15 cell cycle control protein
Microfibrillar-associated protein 1 Chain: K
Molecule details ›
Chain: K
Length: 439 amino acids
Theoretical weight: 52.05 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P55081 (Residues: 1-439; Coverage: 100%)
Gene name: MFAP1
Sequence domains: Microfibril-associated/Pre-mRNA processing
Pleiotropic regulator 1 Chain: G
Molecule details ›
Chain: G
Length: 514 amino acids
Theoretical weight: 57.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43660 (Residues: 1-514; Coverage: 100%)
Gene name: PLRG1
Sequence domains: WD domain, G-beta repeat
Pre-mRNA-processing factor 17 Chain: 8
Molecule details ›
Chain: 8
Length: 579 amino acids
Theoretical weight: 65.61 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O60508 (Residues: 1-579; Coverage: 100%)
Gene names: CDC40, EHB3, PRP17, PRPF17
Sequence domains: WD domain, G-beta repeat
Pre-mRNA-splicing factor 38A Chain: I
Molecule details ›
Chain: I
Length: 312 amino acids
Theoretical weight: 37.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8NAV1 (Residues: 1-312; Coverage: 100%)
Gene name: PRPF38A
Sequence domains:
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:
Pre-mRNA-splicing factor RBM22 Chain: P
Molecule details ›
Chain: P
Length: 420 amino acids
Theoretical weight: 46.96 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NW64 (Residues: 1-420; Coverage: 100%)
Gene names: 199G4, RBM22, ZC3H16
Sequence domains:
SNW domain-containing protein 1 Chain: v
Molecule details ›
Chain: v
Length: 536 amino acids
Theoretical weight: 61.61 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13573 (Residues: 1-536; Coverage: 100%)
Gene names: SKIIP, SKIP, SNW1
Sequence domains: SKIP/SNW domain
Zinc finger matrin-type protein 2 Chain: N
Molecule details ›
Chain: N
Length: 199 amino acids
Theoretical weight: 23.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96NC0 (Residues: 1-199; Coverage: 100%)
Gene name: ZMAT2
Sequence domains: Zinc-finger double-stranded RNA-binding
Ubiquitin-like protein 5 Chain: q
Molecule details ›
Chain: q
Length: 73 amino acids
Theoretical weight: 8.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BZL1 (Residues: 1-73; Coverage: 100%)
Gene name: UBL5
Sequence domains: Ubiquitin family
MINX M3 pre-mRNA Chain: Z
Molecule details ›
Chain: Z
Length: 230 nucleotides
Theoretical weight: 73.71 KDa
U2 snRNA Chain: 2
Molecule details ›
Chain: 2
Length: 188 nucleotides
Theoretical weight: 60.19 KDa
Sequence domains: U2 spliceosomal RNA
U5 snRNA Chain: 5
Molecule details ›
Chain: 5
Length: 116 nucleotides
Theoretical weight: 36.91 KDa
Sequence domains: U5 spliceosomal RNA
U6 snRNA Chain: 6
Molecule details ›
Chain: 6
Length: 106 nucleotides
Theoretical weight: 34.1 KDa
Sequence domains: U6 spliceosomal RNA

Ligands and Environments

3 bound ligands:
Ligand GTP 1 x GTP
Ligand MG 1 x MG
Ligand KGN 1 x KGN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.2Å
Relevant EMDB volumes: EMD-11693

Quick links

Citations

9 review citations

Biology of the mRNA Splicing Machinery and Its Dysregulation in Cancer Providing Therapeutic Opportunities.
Blijlevens et al. (2021)
8 more