› 8qpe

Electron Microscopy
3.1Å resolution

Cryo-EM Structure of Pre-B-like Complex (core part)

Released:
DOI: 10.2210/pdb8qpe/pdb
PDB entry 8qpe coloured by chain, front view.
PDB entry 8qpe coloured by chain, side view.
PDB entry 8qpe coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into the cross-exon to cross-intron spliceosome switch.
Zhang Z, Kumar V, Dybkov O, Will CL, Zhong J, Ludwig SEJ, Urlaub H, Kastner B, Stark H, Lührmann R
OpenAccess logo Nature (2024)
PMID: 38778104
Related structures: EMD-18548

Function and Biology Details

Reaction catalysed: 
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero icosamer (preferred)
PDBe Complex ID:
PDB-CPX-244535 (preferred)
Entry contents:
15 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (20 distinct):
Splicing factor 3A subunit 1 Chain: 7
Molecule details ›
Chain: 7
Length: 793 amino acids
Theoretical weight: 88.99 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15459 (Residues: 1-793; Coverage: 100%)
Gene names: SAP114, SF3A1
Sequence domains:
116 kDa U5 small nuclear ribonucleoprotein component Chain: C
Molecule details ›
Chain: C
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:
Thioredoxin-like protein 4A Chain: D
Molecule details ›
Chain: D
Length: 142 amino acids
Theoretical weight: 16.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P83876 (Residues: 1-142; Coverage: 100%)
Gene names: DIM1, TXNL4, TXNL4A
Sequence domains: Mitosis protein DIM1
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:
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
NHP2-like protein 1 Chain: M
Molecule details ›
Chain: M
Length: 128 amino acids
Theoretical weight: 14.19 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P55769 (Residues: 1-128; Coverage: 100%)
Gene names: NHP2L1, SNU13
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Ubiquitin carboxyl-terminal hydrolase 39 Chain: U
Molecule details ›
Chain: U
Length: 565 amino acids
Theoretical weight: 65.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q53GS9 (Residues: 1-565; Coverage: 100%)
Gene names: CGI-21, HSPC332, PRO2855, USP39
Sequence domains:
WW domain-binding protein 4 Chain: X
Molecule details ›
Chain: X
Length: 376 amino acids
Theoretical weight: 42.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75554 (Residues: 1-376; Coverage: 100%)
Gene names: FBP21, FNBP21, WBP4
Sequence domains:
Zinc finger matrin-type protein 2 Chain: r
Molecule details ›
Chain: r
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
U4/U6 small nuclear ribonucleoprotein Prp3 Chain: J
Molecule details ›
Chain: J
Length: 683 amino acids
Theoretical weight: 77.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43395 (Residues: 1-683; Coverage: 100%)
Gene names: HPRP3, PRP3, PRPF3
Sequence domains:
U4/U6 small nuclear ribonucleoprotein Prp31 Chain: L
Molecule details ›
Chain: L
Length: 499 amino acids
Theoretical weight: 55.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8WWY3 (Residues: 1-499; Coverage: 100%)
Gene names: PRP31, PRPF31
Sequence domains:
U4/U6 small nuclear ribonucleoprotein Prp4 Chain: F
Molecule details ›
Chain: F
Length: 522 amino acids
Theoretical weight: 58.54 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43172 (Residues: 1-522; Coverage: 100%)
Gene names: PRP4, PRPF4
Sequence domains:
Pre-mRNA-processing factor 6 Chain: N
Molecule details ›
Chain: N
Length: 941 amino acids
Theoretical weight: 107.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O94906 (Residues: 1-941; Coverage: 100%)
Gene names: C20orf14, PRPF6
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:
U4/U6.U5 tri-snRNP-associated protein 1 Chain: S
Molecule details ›
Chain: S
Length: 800 amino acids
Theoretical weight: 90.41 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43290 (Residues: 1-800; Coverage: 100%)
Gene name: SART1
Sequence domains:
U4 snRNA Chain: 4
Molecule details ›
Chain: 4
Length: 144 nucleotides
Theoretical weight: 46.18 KDa
Sequence domains: U4 spliceosomal RNA
U5 snRNA Chain: 5
Molecule details ›
Chain: 5
Length: 117 nucleotides
Theoretical weight: 37.25 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
oligo1 Chain: z1
Molecule details ›
Chain: z1
Length: 11 nucleotides
Theoretical weight: 3.56 KDa
oligo2 Chain: z2
Molecule details ›
Chain: z2
Length: 4 nucleotides
Theoretical weight: 1.3 KDa

Ligands and Environments

1 bound ligand:
Ligand IHP 1 x IHP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-18548

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