› 6qdv

Electron Microscopy
3.3Å resolution

Human post-catalytic P complex spliceosome

Released:
DOI: 10.2210/pdb6qdv/pdb
PDB entry 6qdv coloured by chain, front view.
PDB entry 6qdv coloured by chain, side view.
PDB entry 6qdv coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A human postcatalytic spliceosome structure reveals essential roles of metazoan factors for exon ligation.
Fica SM, Oubridge C, Wilkinson ME, Newman AJ, Nagai K
Science 363 710-714 (2019)
PMID: 30705154
Related structures: EMD-4525

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
Peptidylproline (omega=180) = peptidylproline (omega=0)
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 54-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129049 (preferred)
Entry contents:
39 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (44 distinct):
Eukaryotic initiation factor 4A-III Chain: 7
Molecule details ›
Chain: 7
Length: 390 amino acids
Theoretical weight: 44.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P38919 (Residues: 22-404; Coverage: 93%)
Gene names: DDX48, EIF4A3, KIAA0111
Sequence domains:
RNA-binding protein 8A Chain: 8
Molecule details ›
Chain: 8
Length: 91 amino acids
Theoretical weight: 10.37 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y5S9 (Residues: 64-150; Coverage: 50%)
Gene names: HSPC114, MDS014, RBM8, RBM8A
Sequence domains: RNA recognition motif
Protein mago nashi homolog 2 Chain: 9
Molecule details ›
Chain: 9
Length: 144 amino acids
Theoretical weight: 16.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96A72 (Residues: 5-145; Coverage: 95%)
Gene names: MAGOH2, MAGOHB
Sequence domains: Mago nashi protein
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:
U5 small nuclear ribonucleoprotein 200 kDa helicase Chain: B
Molecule details ›
Chain: B
Length: 1722 amino acids
Theoretical weight: 197.05 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75643 (Residues: 404-2125; Coverage: 81%)
Gene names: ASCC3L1, BRR2, HELIC2, KIAA0788, SNRNP200
Sequence domains:
116 kDa U5 small nuclear ribonucleoprotein component Chain: C
Molecule details ›
Chain: C
Length: 899 amino acids
Theoretical weight: 101.23 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15029 (Residues: 56-955; Coverage: 93%)
Gene names: EFTUD2, KIAA0031, SNRP116
Sequence domains:
PRKR-interacting protein 1 Chain: D
Molecule details ›
Chain: D
Length: 123 amino acids
Theoretical weight: 14.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9H875 (Residues: 20-139; Coverage: 65%)
Gene name: PRKRIP1
Sequence domains: Protein of unknown function (DUF1168)
Splicing factor Cactin Chain: F
Molecule details ›
Chain: F
Length: 122 amino acids
Theoretical weight: 15.21 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8WUQ7 (Residues: 637-758; Coverage: 16%)
Gene names: C19orf29, CACTIN
Sequence domains: Cactus-binding C-terminus of cactin protein
Protein FAM32A Chain: G
Molecule details ›
Chain: G
Length: 60 amino acids
Theoretical weight: 7.27 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y421 (Residues: 53-112; Coverage: 54%)
Gene names: CGI-144, FAM32A, OTAG12
Sequence domains: FAM32A
Pre-mRNA-splicing factor CWC22 homolog Chain: H
Molecule details ›
Chain: H
Length: 908 amino acids
Theoretical weight: 105.65 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9HCG8 (Residues: 1-908; Coverage: 100%)
Gene names: CWC22, KIAA1604, NCM
Sequence domains:
Pleiotropic regulator 1 Chain: J
Molecule details ›
Chain: J
Length: 320 amino acids
Theoretical weight: 35.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43660 (Residues: 185-504; Coverage: 62%)
Gene name: PLRG1
Sequence domains: WD domain, G-beta repeat
SNW domain-containing protein 1 Chain: K
Molecule details ›
Chain: K
Length: 295 amino acids
Theoretical weight: 33.82 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13573 (Residues: 41-329; Coverage: 54%)
Gene names: SKIIP, SKIP, SNW1
Sequence domains: SKIP/SNW domain
Protein BUD31 homolog Chain: L
Molecule details ›
Chain: L
Length: 144 amino acids
Theoretical weight: 17.03 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P41223 (Residues: 1-144; Coverage: 100%)
Gene names: BUD31, EDG2
Sequence domains: Pre-mRNA-splicing factor BUD31
Pre-mRNA-splicing factor RBM22 Chain: M
Molecule details ›
Chain: M
Length: 289 amino acids
Theoretical weight: 33.16 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NW64 (Residues: 18-306; Coverage: 69%)
Gene names: 199G4, RBM22, ZC3H16
Sequence domains:
U5 small nuclear ribonucleoprotein 40 kDa protein Chain: N
Molecule details ›
Chain: N
Length: 306 amino acids
Theoretical weight: 34.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96DI7 (Residues: 51-357; Coverage: 86%)
Gene names: PRP8BP, SFP38, SNRNP40, WDR57
Sequence domains: WD domain, G-beta repeat
Cell division cycle 5-like protein Chain: O
Molecule details ›
Chain: O
Length: 802 amino acids
Theoretical weight: 92.41 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q99459 (Residues: 1-802; Coverage: 100%)
Gene names: CDC5L, KIAA0432, PCDC5RP
Sequence domains:
Spliceosome-associated protein CWC15 homolog Chain: P
Molecule details ›
Chain: P
Length: 229 amino acids
Theoretical weight: 26.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9P013 (Residues: 1-229; Coverage: 100%)
Gene names: AD-002, C11orf5, CWC15, HSPC148
Sequence domains: Cwf15/Cwc15 cell cycle control protein
Serine/arginine repetitive matrix protein 2 Chain: R
Molecule details ›
Chain: R
Length: 26 amino acids
Theoretical weight: 2.77 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UQ35 (Residues: 1-26; Coverage: 1%)
Gene names: HSPC075, KIAA0324, SRL300, SRM300, SRRM2
Crooked neck-like protein 1 Chain: S
Molecule details ›
Chain: S
Length: 848 amino acids
Theoretical weight: 100.61 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BZJ0 (Residues: 1-848; Coverage: 100%)
Gene names: CGI-201, CRN, CRNKL1, MSTP021
Sequence domains: HAT (Half-A-TPR) repeat
Pre-mRNA-splicing factor SYF1 Chain: T
Molecule details ›
Chain: T
Length: 855 amino acids
Theoretical weight: 100.15 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9HCS7 (Residues: 1-855; Coverage: 100%)
Gene names: HCNP, KIAA1177, PP3898, SYF1, XAB2
Sequence domains: Tetratricopeptide repeat
RNA helicase aquarius Chain: U
Molecule details ›
Chain: U
Length: 1485 amino acids
Theoretical weight: 171.5 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O60306 (Residues: 1-1485; Coverage: 100%)
Gene names: AQR, KIAA0560
Sequence domains:
ATP-dependent RNA helicase DHX8 Chain: V
Molecule details ›
Chain: V
Length: 1220 amino acids
Theoretical weight: 139.52 KDa
Source organism: Homo sapiens
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q14562 (Residues: 1-1220; Coverage: 100%)
Gene names: DDX8, DHX8
Sequence domains:
U2 small nuclear ribonucleoprotein A' Chain: W
Molecule details ›
Chain: W
Length: 162 amino acids
Theoretical weight: 18.7 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P09661 (Residues: 2-162; Coverage: 63%)
Gene name: SNRPA1
Sequence domains: Leucine-rich repeat
U2 small nuclear ribonucleoprotein B" Chain: Y
Molecule details ›
Chain: Y
Length: 92 amino acids
Theoretical weight: 10.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08579 (Residues: 3-94; Coverage: 41%)
Gene name: SNRPB2
Sequence domains: RNA recognition motif
NF-kappa-B-activating protein Chain: Z
Molecule details ›
Chain: Z
Length: 30 amino acids
Theoretical weight: 3.32 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8N5F7 (Residues: 329-358; Coverage: 7%)
Gene name: NKAP
Small nuclear ribonucleoprotein-associated proteins B and B' Chains: b, k
Molecule details ›
Chains: b, k
Length: 82 amino acids
Theoretical weight: 9.55 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P14678 (Residues: 6-87; Coverage: 34%)
Gene names: COD, SNRPB, SNRPB1
Sequence domains: LSM domain
Pre-mRNA-splicing factor SLU7 Chain: c
Molecule details ›
Chain: c
Length: 586 amino acids
Theoretical weight: 68.51 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95391 (Residues: 1-586; Coverage: 100%)
Gene name: SLU7
Sequence domains: Pre-mRNA splicing Prp18-interacting factor
Small nuclear ribonucleoprotein Sm D3 Chains: d, n
Molecule details ›
Chains: d, n
Length: 84 amino acids
Theoretical weight: 9.46 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62318 (Residues: 2-85; Coverage: 67%)
Gene name: SNRPD3
Sequence domains: LSM domain
Small nuclear ribonucleoprotein E Chains: e, p
Molecule details ›
Chains: e, p
Length: 81 amino acids
Theoretical weight: 9.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62304 (Residues: 11-91; Coverage: 88%)
Gene name: SNRPE
Sequence domains: LSM domain
Small nuclear ribonucleoprotein F Chains: f, q
Molecule details ›
Chains: f, q
Length: 72 amino acids
Theoretical weight: 8.04 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62306 (Residues: 4-75; Coverage: 84%)
Gene names: PBSCF, SNRPF
Sequence domains: LSM domain
Small nuclear ribonucleoprotein G Chains: g, r
Molecule details ›
Chains: g, r
Length: 73 amino acids
Theoretical weight: 8.16 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62308 (Residues: 4-76; Coverage: 96%)
Gene names: PBSCG, SNRPG
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D1 Chains: h, l
Molecule details ›
Chains: h, l
Length: 80 amino acids
Theoretical weight: 9.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62314 (Residues: 1-78; Coverage: 66%)
Gene name: SNRPD1
Sequence domains: LSM domain
Peptidyl-prolyl cis-trans isomerase-like 1 Chain: i
Molecule details ›
Chain: i
Length: 164 amino acids
Theoretical weight: 18.06 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y3C6 (Residues: 3-164; Coverage: 98%)
Gene names: CGI-124, CYPL1, PPIL1, UNQ2425/PRO4984
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
Small nuclear ribonucleoprotein Sm D2 Chains: j, m
Molecule details ›
Chains: j, m
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
Pre-mRNA-processing factor 17 Chain: o
Molecule details ›
Chain: o
Length: 513 amino acids
Theoretical weight: 59.12 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O60508 (Residues: 67-579; Coverage: 89%)
Gene names: CDC40, EHB3, PRP17, PRPF17
Sequence domains: WD domain, G-beta repeat
Pre-mRNA-splicing factor SPF27 Chain: s
Molecule details ›
Chain: s
Length: 225 amino acids
Theoretical weight: 26.16 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75934 (Residues: 1-225; Coverage: 100%)
Gene names: BCAS2, DAM1
Sequence domains: Breast carcinoma amplified sequence 2 (BCAS2)
Pre-mRNA-processing factor 19 Chains: t, u, v, w
Molecule details ›
Chains: t, u, v, w
Length: 504 amino acids
Theoretical weight: 55.25 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UMS4 (Residues: 1-504; Coverage: 100%)
Gene names: NMP200, PRP19, PRPF19, SNEV
Sequence domains:
Pre-mRNA-splicing factor SYF2 Chain: y
Molecule details ›
Chain: y
Length: 144 amino acids
Theoretical weight: 17.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95926 (Residues: 100-239; Coverage: 58%)
Gene names: CBPIN, GCIPIP, SYF2
Sequence domains: SYF2 splicing factor
Splicing regulator SDE2 Chain: z
Molecule details ›
Chain: z
Length: 34 amino acids
Theoretical weight: 4.04 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6IQ49 (Residues: 93-126; Coverage: 8%)
Gene names: C1orf55, SDE2
Sequence domains: Silencing defective 2 N-terminal ubiquitin domain
U2 snRNA Chain: 2
Molecule details ›
Chain: 2
Length: 189 nucleotides
Theoretical weight: 60.46 KDa
Sequence domains: U2 spliceosomal RNA
U5 snRNA Chain: 5
Molecule details ›
Chain: 5
Length: 116 nucleotides
Theoretical weight: 36.91 KDa
Sequence domains: U5 spliceosomal RNA
U6 snRNA Chain: 6
Molecule details ›
Chain: 6
Length: 106 nucleotides
Theoretical weight: 34.1 KDa
Sequence domains: U6 spliceosomal RNA
Ligated exons: MINX mRNA Chain: E
Molecule details ›
Chain: E
Length: 14 nucleotides
Theoretical weight: 4.44 KDa
Intron lariat: MINX RNA Chain: I
Molecule details ›
Chain: I
Length: 113 nucleotides
Theoretical weight: 27.77 KDa

Ligands and Environments

6 bound ligands:
Ligand MG 7 x MG
Ligand K 1 x K
Ligand ATP 1 x ATP
Ligand GTP 1 x GTP
Ligand ZN 7 x ZN
Ligand IHP 1 x IHP
1 modified residue:
Ligand SEP 2 x SEP

Experiments and Validation Details

Entry percentile scores
Resolution: 3.3Å
Relevant EMDB volumes: EMD-4525
Expression system: Saccharomyces cerevisiae

Quick links

Citations

12 review citations

Roles and mechanisms of alternative splicing in cancer - implications for care.
Bonnal et al. (2020)
11 more

10 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)
9 more