› 5z57

Electron Microscopy
6.5Å resolution

Cryo-EM structure of the human activated spliceosome (late Bact) at 6.5 angstrom

Released:
DOI: 10.2210/pdb5z57/pdb
PDB entry 5z57 coloured by chain, front view.
PDB entry 5z57 coloured by chain, side view.
PDB entry 5z57 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of the human activated spliceosome in three conformational states.
Zhang X, Yan C, Zhan X, Li L, Lei J, Shi Y
Cell Res 28 307-322 (2018)
PMID: 29360106
Related structures: EMD-6890

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
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
Peptidylproline (omega=180) = peptidylproline (omega=0)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 57-mer (preferred)
PDBe Complex ID:
PDB-CPX-129047 (preferred)
Entry contents:
43 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (47 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
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
Splicing factor 3A subunit 3 Chain: w
Molecule details ›
Chain: w
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:
Splicing factor 3A subunit 1 Chain: u
Molecule details ›
Chain: u
Length: 793 amino acids
Theoretical weight: 88.99 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15459 (Residues: 1-793; Coverage: 100%)
Gene names: SAP114, SF3A1
Sequence domains:
Splicing factor 3A subunit 2 Chain: v
Molecule details ›
Chain: v
Length: 464 amino acids
Theoretical weight: 49.33 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15428 (Residues: 1-464; Coverage: 100%)
Gene names: SAP62, SF3A2
Sequence domains:
Splicing factor 3B subunit 1 Chain: 1
Molecule details ›
Chain: 1
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
Splicing factor 3B subunit 2 Chain: 2
Molecule details ›
Chain: 2
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:
Splicing factor 3B subunit 3 Chain: 3
Molecule details ›
Chain: 3
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:
Splicing factor 3B subunit 4 Chain: 4
Molecule details ›
Chain: 4
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
Splicing factor 3B subunit 6 Chain: 5
Molecule details ›
Chain: 5
Length: 125 amino acids
Theoretical weight: 14.61 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y3B4 (Residues: 1-125; Coverage: 100%)
Gene names: CGI-110, HSPC175, HT006, SAP14, SF3B14, SF3B14A, SF3B6
Sequence domains: RNA recognition motif
PHD finger-like domain-containing protein 5A Chain: 6
Molecule details ›
Chain: 6
Length: 110 amino acids
Theoretical weight: 12.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q7RTV0 (Residues: 1-110; Coverage: 100%)
Gene name: PHF5A
Sequence domains: PHF5-like protein
Splicing factor 3B subunit 5 Chain: 7
Molecule details ›
Chain: 7
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)
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
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-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:
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)
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
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:
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
Skip Chain: R
Molecule details ›
Chain: R
Length: 540 amino acids
Theoretical weight: 62.06 KDa
Source organism: Homo sapiens
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
Smad nuclear-interacting protein 1 Chain: X
Molecule details ›
Chain: X
Length: 396 amino acids
Theoretical weight: 45.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8TAD8 (Residues: 1-396; Coverage: 100%)
Gene name: SNIP1
Sequence domains: FHA domain
RNA-binding motif protein, X-linked 2 Chain: Y
Molecule details ›
Chain: Y
Length: 322 amino acids
Theoretical weight: 37.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y388 (Residues: 1-322; Coverage: 100%)
Gene names: CGI-79, RBMX2
Sequence domains: RNA recognition motif
BUD13 homolog Chain: Z
Molecule details ›
Chain: Z
Length: 619 amino acids
Theoretical weight: 70.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BRD0 (Residues: 1-619; Coverage: 100%)
Gene name: BUD13
Sequence domains: Pre-mRNA-splicing factor of RES complex
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 Chain: x
Molecule details ›
Chain: x
Length: 1041 amino acids
Theoretical weight: 119.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O60231 (Residues: 1-1041; Coverage: 100%)
Gene names: DBP2, DDX16, DHX16, KIAA0577, PRP2
Sequence domains:
Peptidyl-prolyl cis-trans isomerase E Chain: y
Molecule details ›
Chain: y
Length: 301 amino acids
Theoretical weight: 33.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UNP9 (Residues: 1-301; Coverage: 100%)
Gene names: CYP33, PPIE
Sequence domains:
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: 274 nucleotides
Theoretical weight: 87.89 KDa
U2 snRNA Chain: H
Molecule details ›
Chain: H
Length: 188 nucleotides
Theoretical weight: 60.19 KDa
Sequence domains: U2 spliceosomal RNA

Ligands and Environments

5 bound ligands:
Ligand IHP 1 x IHP
Ligand ALA 1 x ALA
Ligand GTP 1 x GTP
Ligand MG 6 x MG
Ligand ZN 10 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 6.5Å
Relevant EMDB volumes: EMD-6890

Quick links

Citations

29 review citations

Structural Insights into Nuclear pre-mRNA Splicing in Higher Eukaryotes.
Kastner et al. (2019)
28 more

7 mentions without citation

RNAs in the spliceosome: Insight from cryoEM structures.
Zhang et al. (2019)
6 more