› 8qp9

Electron Microscopy
4.1Å resolution

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

Released:
DOI: 10.2210/pdb8qp9/pdb
PDB entry 8qp9 coloured by chain, front view.
PDB entry 8qp9 coloured by chain, side view.
PDB entry 8qp9 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
Nature (2024)
PMID: 38778104
Related structures: EMD-18545

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
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 hexadecamer (preferred)
PDBe Complex ID:
PDB-CPX-244539 (preferred)
Entry contents:
13 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (16 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:
U5 small nuclear ribonucleoprotein 200 kDa helicase Chain: B
Molecule details ›
Chain: B
Length: 2136 amino acids
Theoretical weight: 244.82 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75643 (Residues: 1-2136; Coverage: 100%)
Gene names: ASCC3L1, BRR2, HELIC2, KIAA0788, SNRNP200
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
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:
RNA-binding protein 42 Chain: R
Molecule details ›
Chain: R
Length: 480 amino acids
Theoretical weight: 50.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BTD8 (Residues: 1-480; Coverage: 100%)
Gene name: RBM42
Sequence domains: RNA recognition motif
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:
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:
U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein Chain: X
Molecule details ›
Chain: X
Length: 155 amino acids
Theoretical weight: 18.92 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8WVK2 (Residues: 1-155; Coverage: 100%)
Gene name: SNRNP27
Sequence domains: U4/U6.U5 small nuclear ribonucleoproteins
Probable ATP-dependent RNA helicase DDX23 Chain: G
Molecule details ›
Chain: G
Length: 820 amino acids
Theoretical weight: 95.79 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BUQ8 (Residues: 1-820; Coverage: 100%)
Gene name: DDX23
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-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:
U6 snRNA Chain: 6
Molecule details ›
Chain: 6
Length: 106 nucleotides
Theoretical weight: 34.1 KDa
Sequence domains: U6 spliceosomal RNA
U5 snRNA Chain: 5
Molecule details ›
Chain: 5
Length: 117 nucleotides
Theoretical weight: 37.25 KDa
Sequence domains: U5 spliceosomal RNA
U4 snRNA Chain: 4
Molecule details ›
Chain: 4
Length: 144 nucleotides
Theoretical weight: 46.18 KDa
Sequence domains: U4 spliceosomal RNA

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 4.1Å
Relevant EMDB volumes: EMD-18545

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