› 7abf

Electron Microscopy
3.9Å resolution

Human pre-Bact-1 spliceosome core structure

Released:
DOI: 10.2210/pdb7abf/pdb
PDB entry 7abf coloured by chain, front view.
PDB entry 7abf coloured by chain, side view.
PDB entry 7abf 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-11694

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentadecamer (preferred)
PDBe Complex ID:
PDB-CPX-127126 (preferred)
Entry contents:
12 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (15 distinct):
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
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:
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:
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
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
WW domain-binding protein 11 Chain: X
Molecule details ›
Chain: X
Length: 641 amino acids
Theoretical weight: 70.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y2W2 (Residues: 1-641; Coverage: 100%)
Gene names: NPWBP, SIPP1, SNP70, WBP11
Sequence domains: WW domain binding protein 11
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
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
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
Transcription elongation regulator 1 Chain: A4
Molecule details ›
Chain: A4
Length: 1077 amino acids
Theoretical weight: 121.87 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O14776 (Residues: 1-1098; Coverage: 98%)
Gene names: CA150, TAF2S, TCERG1
Sequence domains:
U5 small nuclear RNA Chain: 5
Molecule details ›
Chain: 5
Length: 116 nucleotides
Theoretical weight: 36.91 KDa
Sequence domains: U5 spliceosomal RNA
U6 small nuclear RNA Chain: 6
Molecule details ›
Chain: 6
Length: 106 nucleotides
Theoretical weight: 34.1 KDa
Sequence domains: U6 spliceosomal RNA
MINX M3 RNA Chain: Z
Molecule details ›
Chain: Z
Length: 230 nucleotides
Theoretical weight: 73.71 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-11694

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

4 mentions without citation

ARID1A Mutations Promote P300-Dependent Endometrial Invasion through Super-Enhancer Hyperacetylation.
Wilson et al. (2020)
3 more