› 6qx9

Electron Microscopy
3.28Å resolution

Structure of a human fully-assembled precatalytic spliceosome (pre-B complex).

Released:
DOI: 10.2210/pdb6qx9/pdb
PDB 6qx9 coloured by chain and viewed from the front.
PDB 6qx9 coloured by chain and viewed from the side.
PDB 6qx9 coloured by chain and viewed from the top.
Source organisms:
Primary publication:
Mechanism of 5' splice site transfer for human spliceosome activation.
Charenton C, Wilkinson ME, Nagai K
Science (2019)
PMID: 30975767
Related structures: EMD-4665

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 71-mer (preferred)
Entry contents:
44 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (50 distinct):
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
Splicing factor 3B subunit 4 Chain: B4
Molecule details ›
Chain: B4
Length: 424 amino acids
Theoretical weight: 44.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15427 (Residues: 1-424; Coverage: 100%)
Gene names: SAP49, SF3B4
Sequence domains: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
Small nuclear ribonucleoprotein Sm D3 Chains: 13, 23, 43, 53
Molecule details ›
Chains: 13, 23, 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 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:
Small nuclear ribonucleoprotein E Chains: 1e, 2e, 4e, 5e
Molecule details ›
Chains: 1e, 2e, 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
U1 small nuclear ribonucleoprotein 70 kDa Chain: 1K
Molecule details ›
Chain: 1K
Length: 437 amino acids
Theoretical weight: 51.68 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08621 (Residues: 1-437; Coverage: 100%)
Gene names: RNPU1Z, RPU1, SNRNP70, SNRP70, U1AP1
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:
Small nuclear ribonucleoprotein Sm D1 Chains: 11, 21, 41, 51
Molecule details ›
Chains: 11, 21, 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
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. (a.k.a. RRM, RBD, or RNP domain)
Small nuclear ribonucleoprotein F Chains: 1f, 2f, 4f, 5f
Molecule details ›
Chains: 1f, 2f, 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
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
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 D2 Chains: 12, 22, 42, 52
Molecule details ›
Chains: 12, 22, 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
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 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
U2 small nuclear ribonucleoprotein B'' Chain: 2B
Molecule details ›
Chain: 2B
Length: 225 amino acids
Theoretical weight: 25.52 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08579 (Residues: 1-225; Coverage: 100%)
Gene name: SNRPB2
Sequence domains: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
Splicing factor 3A subunit 2 Chain: A2
Molecule details ›
Chain: A2
Length: 209 amino acids
Theoretical weight: 24.34 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15428 (Residues: 1-209; Coverage: 45%)
Gene names: SAP62, SF3A2
Sequence domains:
Splicing factor 3B subunit 2 Chain: B2
Molecule details ›
Chain: B2
Length: 895 amino acids
Theoretical weight: 100.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13435 (Residues: 1-895; Coverage: 100%)
Gene names: SAP145, SF3B2
Sequence domains:
116 kDa U5 small nuclear ribonucleoprotein component Chain: 5C
Molecule details ›
Chain: 5C
Length: 854 amino acids
Theoretical weight: 95.97 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15029 (Residues: 104-957; Coverage: 88%)
Gene names: EFTUD2, KIAA0031, SNRP116
Sequence domains:
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:
Small nuclear ribonucleoprotein-associated proteins B and B' Chains: 1b, 2b, 4b, 5b
Molecule details ›
Chains: 1b, 2b, 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
Splicing factor 3B subunit 5 Chain: B5
Molecule details ›
Chain: B5
Length: 86 amino acids
Theoretical weight: 10.15 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BWJ5 (Residues: 1-86; Coverage: 100%)
Gene names: SF3B10, SF3B5
Sequence domains: Splicing factor 3B subunit 10 (SF3b10)
U1 small nuclear ribonucleoprotein A Chain: 1A
Molecule details ›
Chain: 1A
Length: 282 amino acids
Theoretical weight: 31.32 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P09012 (Residues: 1-282; Coverage: 100%)
Gene name: SNRPA
Sequence domains: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
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:
Pre-mRNA-processing factor 6 Chain: 5J
Molecule details ›
Chain: 5J
Length: 850 amino acids
Theoretical weight: 97 KDa
Source organisms: UniProt:
  • Canonical: O94906 (Residues: 656-937; Coverage: 30%)
  • Canonical: Q91YR7 (Residues: 18-655; Coverage: 60%)
Gene names: C20orf14, PRPF6, Prpf6
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
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
Splicing factor 3B subunit 3 Chain: B3
Molecule details ›
Chain: B3
Length: 1217 amino acids
Theoretical weight: 135.72 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15393 (Residues: 1-1217; Coverage: 100%)
Gene names: KIAA0017, SAP130, SF3B3
Sequence domains:
Small nuclear ribonucleoprotein G Chains: 1g, 2g, 4g, 5g
Molecule details ›
Chains: 1g, 2g, 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
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
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:
Splicing factor 3A subunit 3 Chain: A3
Molecule details ›
Chain: A3
Length: 501 amino acids
Theoretical weight: 58.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q12874 (Residues: 1-501; Coverage: 100%)
Gene names: SAP61, SF3A3
Sequence domains:
U4/U6.U5 tri-snRNP-associated protein 2 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:
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
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
PHD finger-like domain-containing protein 5A Chain: BP
Molecule details ›
Chain: BP
Length: 104 amino acids
Theoretical weight: 11.64 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q7RTV0 (Residues: 1-104; Coverage: 95%)
Gene name: PHF5A
Sequence domains: PHF5-like protein
U1 small nuclear ribonucleoprotein C Chain: 1C
Molecule details ›
Chain: 1C
Length: 159 amino acids
Theoretical weight: 17.42 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P09234 (Residues: 1-159; Coverage: 100%)
Gene name: SNRPC
Sequence domains: U1 zinc finger
Serine/threonine-protein kinase PRP4 homolog Chain: K
Molecule details ›
Chain: K
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, PRP4H, PRP4K, PRPF4B
Sequence domains: Protein kinase 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:
U2 small nuclear ribonucleoprotein A' Chain: 2A
Molecule details ›
Chain: 2A
Length: 255 amino acids
Theoretical weight: 28.46 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P09661 (Residues: 1-255; Coverage: 100%)
Gene name: SNRPA1
Sequence domains: Leucine-rich repeat
Splicing factor 3A subunit 1 Chain: A1
Molecule details ›
Chain: A1
Length: 647 amino acids
Theoretical weight: 71.62 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15459 (Residues: 1-793; Coverage: 82%)
Gene names: SAP114, SF3A1
Sequence domains:
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
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:
Splicing factor 3B subunit 1 Chain: B1
Molecule details ›
Chain: B1
Length: 1304 amino acids
Theoretical weight: 146.02 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75533 (Residues: 1-1304; Coverage: 100%)
Gene names: SAP155, SF3B1
Sequence domains: Splicing factor 3B subunit 1
U1 snRNA Chain: 1
Molecule details ›
Chain: 1
Length: 164 nucleotides
Theoretical weight: 52.7 KDa
Sequence domains: U1 spliceosomal RNA
U6 snRNA Chain: 6
Molecule details ›
Chain: 6
Length: 106 nucleotides
Theoretical weight: 34.1 KDa
Sequence domains: U6 spliceosomal RNA
AdML pre-mRNA Chain: I
Molecule details ›
Chain: I
Length: 62 nucleotides
Theoretical weight: 15.28 KDa
U5 snRNA Chain: 5
Molecule details ›
Chain: 5
Length: 117 nucleotides
Theoretical weight: 37.25 KDa
Sequence domains: U5 spliceosomal RNA
U2 snRNA Chain: 2
Molecule details ›
Chain: 2
Length: 188 nucleotides
Theoretical weight: 60.17 KDa
Sequence domains: U2 spliceosomal RNA
U4 snRNA Chain: 4
Molecule details ›
Chain: 4
Length: 146 nucleotides
Theoretical weight: 47 KDa
Sequence domains: U4 spliceosomal RNA

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.28Å
Relevant EMDB volumes: EMD-4665
Expression system: Saccharomyces cerevisiae

Quick links

Citations

12 review citations

The Role of the m6A RNA Methyltransferase METTL16 in Gene Expression and SAM Homeostasis.
Mermoud JE. (2022)
11 more

17 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)
16 more