› 6qw6

Electron Microscopy
2.92Å resolution

Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution.

Released:
DOI: 10.2210/pdb6qw6/pdb
PDB entry 6qw6 coloured by chain, front view.
PDB entry 6qw6 coloured by chain, side view.
PDB entry 6qw6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanism of 5' splice site transfer for human spliceosome activation.
Charenton C, Wilkinson ME, Nagai K
Science 364 362-367 (2019)
PMID: 30975767
Related structures: EMD-4658

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 39-mer (preferred)
PDBe Complex ID:
PDB-CPX-128859 (preferred)
Entry contents:
29 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (32 distinct):
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
Small nuclear ribonucleoprotein Sm D1 Chains: 41, 51
Molecule details ›
Chains: 41, 51
Length: 119 amino acids
Theoretical weight: 13.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62314 (Residues: 1-119; Coverage: 100%)
Gene name: SNRPD1
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D2 Chains: 42, 52
Molecule details ›
Chains: 42, 52
Length: 118 amino acids
Theoretical weight: 13.55 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62316 (Residues: 1-118; Coverage: 100%)
Gene names: SNRPD1, SNRPD2
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D3 Chains: 43, 53
Molecule details ›
Chains: 43, 53
Length: 126 amino acids
Theoretical weight: 13.94 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62318 (Residues: 1-126; Coverage: 100%)
Gene name: SNRPD3
Sequence domains: LSM domain
U4/U6 small nuclear ribonucleoprotein Prp3 Chain: 4A
Molecule details ›
Chain: 4A
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 Prp4 Chain: 4B
Molecule details ›
Chain: 4B
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:
U4/U6 small nuclear ribonucleoprotein Prp31 Chain: 4C
Molecule details ›
Chain: 4C
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:
NHP2-like protein 1 Chain: 4D
Molecule details ›
Chain: 4D
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
Small nuclear ribonucleoprotein-associated proteins B and B' Chains: 4b, 5b
Molecule details ›
Chains: 4b, 5b
Length: 240 amino acids
Theoretical weight: 24.64 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P14678 (Residues: 1-240; Coverage: 100%)
Gene names: COD, SNRPB, SNRPB1
Sequence domains: LSM domain
Small nuclear ribonucleoprotein E Chains: 4e, 5e
Molecule details ›
Chains: 4e, 5e
Length: 92 amino acids
Theoretical weight: 10.82 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62304 (Residues: 1-92; Coverage: 100%)
Gene name: SNRPE
Sequence domains: LSM domain
Small nuclear ribonucleoprotein F Chains: 4f, 5f
Molecule details ›
Chains: 4f, 5f
Length: 86 amino acids
Theoretical weight: 9.73 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62306 (Residues: 1-86; Coverage: 100%)
Gene names: PBSCF, SNRPF
Sequence domains: LSM domain
Small nuclear ribonucleoprotein G Chains: 4g, 5g
Molecule details ›
Chains: 4g, 5g
Length: 76 amino acids
Theoretical weight: 8.51 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62308 (Residues: 1-76; Coverage: 100%)
Gene names: PBSCG, SNRPG
Sequence domains: LSM domain
Pre-mRNA-processing-splicing factor 8 Chain: 5A
Molecule details ›
Chain: 5A
Length: 2311 amino acids
Theoretical weight: 271.51 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6P2Q9 (Residues: 25-2335; Coverage: 99%)
Gene names: PRPC8, PRPF8
Sequence domains:
U5 small nuclear ribonucleoprotein 200 kDa helicase Chain: 5B
Molecule details ›
Chain: 5B
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: 5C
Molecule details ›
Chain: 5C
Length: 853 amino acids
Theoretical weight: 95.84 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15029 (Residues: 104-956; Coverage: 88%)
Gene names: EFTUD2, KIAA0031, SNRP116
Sequence domains:
Thioredoxin-like protein 4A Chain: 5D
Molecule details ›
Chain: 5D
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-processing factor 6 Chain: 5J
Molecule details ›
Chain: 5J
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:
U5 small nuclear ribonucleoprotein 40 kDa protein Chain: 5O
Molecule details ›
Chain: 5O
Length: 357 amino acids
Theoretical weight: 39.36 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96DI7 (Residues: 1-357; Coverage: 100%)
Gene names: PRP8BP, SFP38, SNRNP40, WDR57
Sequence domains: WD domain, G-beta repeat
Probable ATP-dependent RNA helicase DDX23 Chain: 5X
Molecule details ›
Chain: 5X
Length: 820 amino acids
Theoretical weight: 95.79 KDa
Source organism: Homo sapiens
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q9BUQ8 (Residues: 1-820; Coverage: 100%)
Gene name: DDX23
Sequence domains:
U6 snRNA-associated Sm-like protein LSm2 Chain: 62
Molecule details ›
Chain: 62
Length: 95 amino acids
Theoretical weight: 10.85 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y333 (Residues: 1-95; Coverage: 100%)
Gene names: C6orf28, G7B, LSM2
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm3 Chain: 63
Molecule details ›
Chain: 63
Length: 102 amino acids
Theoretical weight: 11.86 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62310 (Residues: 1-102; Coverage: 100%)
Gene names: LSM3, MDS017
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm4 Chain: 64
Molecule details ›
Chain: 64
Length: 139 amino acids
Theoretical weight: 15.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y4Z0 (Residues: 1-139; Coverage: 100%)
Gene name: LSM4
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm5 Chain: 65
Molecule details ›
Chain: 65
Length: 91 amino acids
Theoretical weight: 9.95 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y4Y9 (Residues: 1-91; Coverage: 100%)
Gene name: LSM5
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm6 Chain: 66
Molecule details ›
Chain: 66
Length: 80 amino acids
Theoretical weight: 9.14 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62312 (Residues: 1-80; Coverage: 100%)
Gene name: LSM6
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm7 Chain: 67
Molecule details ›
Chain: 67
Length: 103 amino acids
Theoretical weight: 11.62 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UK45 (Residues: 1-103; Coverage: 100%)
Gene name: LSM7
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm8 Chain: 68
Molecule details ›
Chain: 68
Length: 96 amino acids
Theoretical weight: 10.41 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95777 (Residues: 1-96; Coverage: 100%)
Gene name: LSM8
Sequence domains: LSM domain
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: 555 amino acids
Theoretical weight: 64.41 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q53GS9 (Residues: 1-555; Coverage: 98%)
Gene names: CGI-21, HSPC332, PRO2855, USP39
Sequence domains:
U4 snRNA Chain: 4
Molecule details ›
Chain: 4
Length: 146 nucleotides
Theoretical weight: 47 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: 88 nucleotides
Theoretical weight: 28.34 KDa
Sequence domains: U6 spliceosomal RNA

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 2.92Å
Relevant EMDB volumes: EMD-4658
Expression system: Saccharomyces cerevisiae

Quick links

Citations

19 review citations

Regulation and Function of RNA Pseudouridylation in Human Cells.
Borchardt et al. (2020)
18 more

6 mentions without citation

Host DDX Helicases as Possible SARS-CoV-2 Proviral Factors: A Structural Overview of Their Hijacking Through Multiple Viral Proteins.
Squeglia et al. (2020)
5 more