› 3jcr

Electron Microscopy
7Å resolution

3D structure determination of the human*U4/U6.U5* tri-snRNP complex

Released:
DOI: 10.2210/pdb3jcr/pdb
PDB entry 3jcr coloured by chain, front view.
PDB entry 3jcr coloured by chain, side view.
PDB entry 3jcr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular architecture of the human U4/U6.U5 tri-snRNP.
Agafonov DE, Kastner B, Dybkov O, Hofele RV, Liu WT, Urlaub H, Lührmann R, Stark H
Science 351 1416-20 (2016)
PMID: 26912367
Related structures: EMD-6581

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 36-mer (preferred)
Entry contents:
26 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (29 distinct):
Pre-mRNA-processing factor 6 Chain: G
Molecule details ›
Chain: G
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: D
Molecule details ›
Chain: D
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
U5 small nuclear ribonucleoprotein 200 kDa helicase Chain: C
Molecule details ›
Chain: C
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:
Thioredoxin-like protein 4A Chain: E
Molecule details ›
Chain: E
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-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:
Probable ATP-dependent RNA helicase DDX23 Chain: F
Molecule details ›
Chain: F
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:
116 kDa U5 small nuclear ribonucleoprotein component Chain: B
Molecule details ›
Chain: B
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:
Small nuclear ribonucleoprotein-associated proteins B and B' Chains: O, o
Molecule details ›
Chains: O, o
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 Sm D1 Chains: P, p
Molecule details ›
Chains: P, p
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: Q, q
Molecule details ›
Chains: Q, q
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: R, r
Molecule details ›
Chains: R, r
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
Small nuclear ribonucleoprotein E Chains: S, s
Molecule details ›
Chains: S, s
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: T, t
Molecule details ›
Chains: T, t
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: U, u
Molecule details ›
Chains: U, u
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
U6 snRNA-associated Sm-like protein LSm8 Chain: 8
Molecule details ›
Chain: 8
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
U6 snRNA-associated Sm-like protein LSm6 Chain: 6
Molecule details ›
Chain: 6
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 LSm5 Chain: 5
Molecule details ›
Chain: 5
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 LSm4 Chain: 4
Molecule details ›
Chain: 4
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 LSm3 Chain: 3
Molecule details ›
Chain: 3
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 LSm2 Chain: 2
Molecule details ›
Chain: 2
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 LSm7 Chain: 7
Molecule details ›
Chain: 7
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
U4/U6 small nuclear ribonucleoprotein Prp3 Chain: K
Molecule details ›
Chain: K
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: L
Molecule details ›
Chain: L
Length: 521 amino acids
Theoretical weight: 58.41 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: J
Molecule details ›
Chain: J
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: I
Molecule details ›
Chain: I
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: V
Molecule details ›
Chain: V
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 snRNA Chain: M
Molecule details ›
Chain: M
Length: 145 nucleotides
Theoretical weight: 46.54 KDa
Sequence domains: U4 spliceosomal RNA
U6 snRNA Chain: N
Molecule details ›
Chain: N
Length: 106 nucleotides
Theoretical weight: 34.1 KDa
Sequence domains: U6 spliceosomal RNA
U5 snRNA Chain: H
Molecule details ›
Chain: H
Length: 116 nucleotides
Theoretical weight: 36.89 KDa
Sequence domains: U5 spliceosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 7Å
Relevant EMDB volumes: EMD-6581

Quick links

Citations

34 review citations

Unravelling biological macromolecules with cryo-electron microscopy.
Fernandez-Leiro et al. (2016)
33 more

11 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)
10 more