› 5xjc

Electron Microscopy
3.6Å resolution

Cryo-EM structure of the human spliceosome just prior to exon ligation at 3.6 angstrom

Released:
DOI: 10.2210/pdb5xjc/pdb
PDB entry 5xjc coloured by chain, front view.
PDB entry 5xjc coloured by chain, side view.
PDB entry 5xjc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
An Atomic Structure of the Human Spliceosome.
Zhang X, Yan C, Hang J, Finci LI, Lei J, Shi Y
Cell 169 918-929.e14 (2017)
PMID: 28502770
Related structures: EMD-6721

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 50-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127362 (preferred)
Entry contents:
36 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (40 distinct):
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:
116 kDa U5 small nuclear ribonucleoprotein component Chain: C
Molecule details ›
Chain: C
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: D
Molecule details ›
Chain: D
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: E
Molecule details ›
Chain: E
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-splicing factor SYF1 Chain: I
Molecule details ›
Chain: I
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
Crooked neck-like protein 1 Chain: J
Molecule details ›
Chain: J
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 SPF27 Chain: K
Molecule details ›
Chain: K
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)
Cell division cycle 5-like protein Chain: L
Molecule details ›
Chain: L
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:
Pre-mRNA-splicing factor SYF2 Chain: M
Molecule details ›
Chain: M
Length: 243 amino acids
Theoretical weight: 28.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95926 (Residues: 1-243; Coverage: 100%)
Gene names: CBPIN, GCIPIP, SYF2
Sequence domains: SYF2 splicing factor
Protein BUD31 homolog Chain: N
Molecule details ›
Chain: N
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: O
Molecule details ›
Chain: O
Length: 420 amino acids
Theoretical weight: 46.96 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NW64 (Residues: 1-420; Coverage: 100%)
Gene names: 199G4, RBM22, ZC3H16
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
RNA helicase aquarius Chain: Q
Molecule details ›
Chain: Q
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:
SNW domain-containing protein 1 Chain: R
Molecule details ›
Chain: R
Length: 536 amino acids
Theoretical weight: 61.77 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13573 (Residues: 1-536; Coverage: 100%)
Gene names: SKIIP, SKIP, SNW1
Sequence domains: SKIP/SNW domain
Peptidyl-prolyl cis-trans isomerase-like 1 Chain: S
Molecule details ›
Chain: S
Length: 166 amino acids
Theoretical weight: 18.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y3C6 (Residues: 1-166; Coverage: 100%)
Gene names: CGI-124, CYPL1, PPIL1, UNQ2425/PRO4984
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
Pleiotropic regulator 1 Chain: T
Molecule details ›
Chain: T
Length: 514 amino acids
Theoretical weight: 57.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43660 (Residues: 1-514; Coverage: 100%)
Gene name: PLRG1
Sequence domains: WD domain, G-beta repeat
Serine/arginine repetitive matrix protein 2 Chain: U
Molecule details ›
Chain: U
Length: 2752 amino acids
Theoretical weight: 300.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UQ35 (Residues: 1-2752; Coverage: 100%)
Gene names: HSPC075, KIAA0324, SRL300, SRM300, SRRM2
Sequence domains: cwf21 domain
Pre-mRNA-splicing factor CWC22 homolog Chain: V
Molecule details ›
Chain: V
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:
Pre-mRNA-processing factor 17 Chain: W
Molecule details ›
Chain: W
Length: 579 amino acids
Theoretical weight: 65.61 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O60508 (Residues: 1-579; Coverage: 100%)
Gene names: CDC40, EHB3, PRP17, PRPF17
Sequence domains: WD domain, G-beta repeat
PRKR-interacting protein 1 Chain: X
Molecule details ›
Chain: X
Length: 184 amino acids
Theoretical weight: 21.04 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9H875 (Residues: 1-184; Coverage: 100%)
Gene name: PRKRIP1
Sequence domains: Protein of unknown function (DUF1168)
ATP-dependent RNA helicase DHX8 Chain: Y
Molecule details ›
Chain: Y
Length: 1220 amino acids
Theoretical weight: 139.51 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q14562 (Residues: 1-1220; Coverage: 100%)
Gene names: DDX8, DHX8
Sequence domains:
Pre-mRNA-splicing factor SLU7 Chain: Z
Molecule details ›
Chain: Z
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: a, h
Molecule details ›
Chains: a, h
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-associated proteins B and B' Chains: b, i
Molecule details ›
Chains: b, i
Length: 231 amino acids
Theoretical weight: 23.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P14678 (Residues: 1-229; Coverage: 95%)
Gene names: COD, SNRPB, SNRPB1
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D1 Chains: c, j
Molecule details ›
Chains: c, j
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: d, k
Molecule details ›
Chains: d, k
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 F Chains: f, m
Molecule details ›
Chains: f, m
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 E Chains: e, l
Molecule details ›
Chains: e, l
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 G Chains: g, n
Molecule details ›
Chains: g, n
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
U2 small nuclear ribonucleoprotein A' Chain: o
Molecule details ›
Chain: o
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
U2 small nuclear ribonucleoprotein B'' Chain: p
Molecule details ›
Chain: p
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
Pre-mRNA-processing factor 19 Chains: q, r, s, t
Molecule details ›
Chains: q, r, s, t
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:
Eukaryotic initiation factor 4A-III Chain: u
Molecule details ›
Chain: u
Length: 411 amino acids
Theoretical weight: 46.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P38919 (Residues: 1-411; Coverage: 100%)
Gene names: DDX48, EIF4A3, KIAA0111
Sequence domains:
Protein mago nashi homolog 2 Chain: v
Molecule details ›
Chain: v
Length: 148 amino acids
Theoretical weight: 17.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96A72 (Residues: 1-148; Coverage: 100%)
Gene names: MAGOH2, MAGOHB
Sequence domains: Mago nashi protein
RNA-binding protein 8A Chain: w
Molecule details ›
Chain: w
Length: 174 amino acids
Theoretical weight: 19.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y5S9 (Residues: 1-174; Coverage: 100%)
Gene names: HSPC114, MDS014, RBM8, RBM8A
Sequence domains: RNA recognition motif
Protein CASC3 Chain: x
Molecule details ›
Chain: x
Length: 703 amino acids
Theoretical weight: 76.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15234 (Residues: 1-703; Coverage: 100%)
Gene names: CASC3, MLN51
Sequence domains: CASC3/Barentsz eIF4AIII binding
U5 snRNA Chain: B
Molecule details ›
Chain: B
Length: 117 nucleotides
Theoretical weight: 37.25 KDa
Sequence domains: U5 spliceosomal RNA
U6 snRNA Chain: F
Molecule details ›
Chain: F
Length: 107 nucleotides
Theoretical weight: 34.4 KDa
Sequence domains: U6 spliceosomal RNA
pre-mRNA Chain: G
Molecule details ›
Chain: G
Length: 275 nucleotides
Theoretical weight: 87.98 KDa
Homo sapiens small nuclear RNA (U2) gene Chain: H
Molecule details ›
Chain: H
Length: 188 nucleotides
Theoretical weight: 60.19 KDa
Sequence domains: U2 spliceosomal RNA

Ligands and Environments

6 bound ligands:
Ligand IHP 1 x IHP
Ligand GTP 1 x GTP
Ligand MG 11 x MG
Ligand ADP 2 x ADP
Ligand ZN 7 x ZN
Ligand ATP 2 x ATP
1 modified residue:
Ligand SEP 2 x SEP

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-6721

Quick links

Citations

36 review citations

Nuclear speckles: molecular organization, biological function and role in disease.
Galganski et al. (2017)
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9 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)
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