› 8y6o

Electron Microscopy
3.38Å resolution

Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U11 and tri-snRNP part

Released:
DOI: 10.2210/pdb8y6o/pdb
PDB entry 8y6o coloured by chain, front view.
PDB entry 8y6o coloured by chain, side view.
PDB entry 8y6o coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome.
Bai R, Yuan M, Zhang P, Luo T, Shi Y, Wan R
Science 383 1245-1252 (2024)
PMID: 38484052
Related structures: EMD-38993

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).
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 46-mer (preferred)
PDBe Complex ID:
PDB-CPX-249732 (preferred)
Entry contents:
27 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (32 distinct):
Pre-mRNA-processing-splicing factor 8 Chain: C
Molecule details ›
Chain: C
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: D
Molecule details ›
Chain: D
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:
U5 small nuclear ribonucleoprotein 200 kDa helicase Chain: E
Molecule details ›
Chain: E
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:
U5 small nuclear ribonucleoprotein 40 kDa protein Chain: F
Molecule details ›
Chain: F
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
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:
Thioredoxin-like protein 4B Chain: H
Molecule details ›
Chain: H
Length: 149 amino acids
Theoretical weight: 17.03 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NX01 (Residues: 1-149; Coverage: 100%)
Gene names: DIM2, DLP, TXNL4B
Sequence domains: Mitosis protein DIM1
Probable ATP-dependent RNA helicase DDX23 Chain: I
Molecule details ›
Chain: I
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:
Small nuclear ribonucleoprotein-associated proteins B and B' Chains: a, h, o
Molecule details ›
Chains: a, h, 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: b, i, p
Molecule details ›
Chains: b, i, 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: c, j, q
Molecule details ›
Chains: c, j, 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: d, k, r
Molecule details ›
Chains: d, k, 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: e, l, s
Molecule details ›
Chains: e, l, 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: f, m, t
Molecule details ›
Chains: f, m, 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: g, n, u
Molecule details ›
Chains: g, n, 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
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: M
Molecule details ›
Chain: M
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 Prp3 Chain: N
Molecule details ›
Chain: N
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:
NHP2-like protein 1 Chain: O
Molecule details ›
Chain: O
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
Centrosomal AT-AC splicing factor Chain: R
Molecule details ›
Chain: R
Length: 332 amino acids
Theoretical weight: 38.03 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q86UT8 (Residues: 1-332; Coverage: 100%)
Gene names: CCDC84, CENATAC, DLNB14
Sequence domains: Coiled coil protein 84
Zinc finger matrin-type protein 5 Chain: V
Molecule details ›
Chain: V
Length: 170 amino acids
Theoretical weight: 20 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UDW3 (Residues: 1-170; Coverage: 100%)
Gene name: ZMAT5
Sequence domains:
U11/U12 small nuclear ribonucleoprotein 35 kDa protein Chain: W
Molecule details ›
Chain: W
Length: 246 amino acids
Theoretical weight: 29.51 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q16560 (Residues: 1-246; Coverage: 100%)
Gene names: HM1, SNRNP35, U1SNRNPBP
Sequence domains: RNA recognition motif
U11/U12 small nuclear ribonucleoprotein 25 kDa protein Chain: X
Molecule details ›
Chain: X
Length: 132 amino acids
Theoretical weight: 15.29 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BV90 (Residues: 1-132; Coverage: 100%)
Gene names: C16orf33, SNRNP25
Sequence domains: Ubiquitin-like domain
U11/U12 small nuclear ribonucleoprotein 48 kDa protein Chain: Y
Molecule details ›
Chain: Y
Length: 339 amino acids
Theoretical weight: 40.04 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6IEG0 (Residues: 1-339; Coverage: 100%)
Gene names: C6orf151, SNRNP48
Sequence domains: U11-48K-like CHHC zinc finger
Programmed cell death protein 7 Chain: Z
Molecule details ›
Chain: Z
Length: 485 amino acids
Theoretical weight: 54.79 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8N8D1 (Residues: 1-485; Coverage: 100%)
Gene name: PDCD7
Sequence domains: Programmed cell death protein 7
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:
Serine/threonine-protein kinase PRP4 homolog Chain: Q
Molecule details ›
Chain: Q
Length: 1007 amino acids
Theoretical weight: 117.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13523 (Residues: 1-1007; Coverage: 100%)
Gene names: KIAA0536, PRP4, PRP4B, PRP4H, PRP4K, PRPF4K
Sequence domains: Protein kinase domain
pre-mRNA Chain: A
Molecule details ›
Chain: A
Length: 280 nucleotides
Theoretical weight: 89.52 KDa
U5 snRNA Chain: B
Molecule details ›
Chain: B
Length: 117 nucleotides
Theoretical weight: 37.25 KDa
Sequence domains: U5 spliceosomal RNA
U4atac snRNA Chain: J
Molecule details ›
Chain: J
Length: 131 nucleotides
Theoretical weight: 42.05 KDa
Sequence domains: U4atac minor spliceosomal RNA
U6atac snRNA Chain: K
Molecule details ›
Chain: K
Length: 125 nucleotides
Theoretical weight: 40.22 KDa
Sequence domains: U6atac minor spliceosomal RNA
U11 snRNA Chain: P
Molecule details ›
Chain: P
Length: 135 nucleotides
Theoretical weight: 43.51 KDa
Sequence domains: U11 spliceosomal RNA

Ligands and Environments

4 bound ligands:
Ligand MG 2 x MG
Ligand IHP 1 x IHP
Ligand GTP 1 x GTP
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.38Å
Relevant EMDB volumes: EMD-38993

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