› 5nrl

Electron Microscopy
7.2Å resolution

Structure of a pre-catalytic spliceosome.

Released:
DOI: 10.2210/pdb5nrl/pdb
PDB entry 5nrl coloured by chain, front view.
PDB entry 5nrl coloured by chain, side view.
PDB entry 5nrl coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structure of a pre-catalytic spliceosome.
Plaschka C, Lin PC, Nagai K
Nature 546 617-621 (2017)
PMID: 28530653
Related structures: EMD-3683

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 58-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-216144 (preferred)
Entry contents:
39 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (44 distinct):
U6 snRNA-associated Sm-like protein LSm3 Chain: 3
Molecule details ›
Chain: 3
Length: 89 amino acids
Theoretical weight: 10.04 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P57743 (Residues: 1-89; Coverage: 100%)
Gene names: LSM3, SMX4, USS2, YLR438C-A
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm7 Chain: 7
Molecule details ›
Chain: 7
Length: 115 amino acids
Theoretical weight: 13.03 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53905 (Residues: 1-115; Coverage: 100%)
Gene names: LSM7, N1202, N1780, YNL147W
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm8 Chain: 8
Molecule details ›
Chain: 8
Length: 109 amino acids
Theoretical weight: 12.4 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P47093 (Residues: 1-109; Coverage: 100%)
Gene names: J1464, LSM8, YJR022W, YJR83.16
Sequence domains: LSM domain
Pre-mRNA-splicing factor 8 Chain: A
Molecule details ›
Chain: A
Length: 2413 amino acids
Theoretical weight: 279.87 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P33334 (Residues: 1-2413; Coverage: 100%)
Gene names: DBF3, DNA39, PRP8, RNA8, SLT21, USA2, YHR165C
Sequence domains:
Pre-mRNA-splicing helicase BRR2 Chain: B
Molecule details ›
Chain: B
Length: 2163 amino acids
Theoretical weight: 246.47 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32639 (Residues: 1-2163; Coverage: 100%)
Gene names: BRR2, RSS1, SNU246, SYGP-ORF66, YER172C
Sequence domains:
Pre-mRNA-splicing factor SNU114 Chain: C
Molecule details ›
Chain: C
Length: 1008 amino acids
Theoretical weight: 114.17 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36048 (Residues: 1-1008; Coverage: 100%)
Gene names: GIN10, SNU114, YKL173W, YKL637
Sequence domains:
Spliceosomal protein DIB1 Chain: D
Molecule details ›
Chain: D
Length: 143 amino acids
Theoretical weight: 16.8 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06819 (Residues: 1-143; Coverage: 100%)
Gene names: CDH1, DIB1, P9513.12, SNU16, YPR082C
Sequence domains: Mitosis protein DIM1
66 kDa U4/U6.U5 small nuclear ribonucleoprotein component Chain: E
Molecule details ›
Chain: E
Length: 587 amino acids
Theoretical weight: 66.54 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12420 (Residues: 1-587; Coverage: 100%)
Gene names: 05667, SNU66, YOR308C
Sequence domains:
Pre-mRNA-processing factor 31 Chain: F
Molecule details ›
Chain: F
Length: 494 amino acids
Theoretical weight: 56.38 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P49704 (Residues: 1-494; Coverage: 100%)
Gene names: PRP31, YGR091W
Sequence domains:
U4/U6 small nuclear ribonucleoprotein PRP3 Chain: G
Molecule details ›
Chain: G
Length: 469 amino acids
Theoretical weight: 55.97 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03338 (Residues: 1-469; Coverage: 100%)
Gene names: D8035.16, PRP3, RNA3, YDR473C
Sequence domains:
U4/U6 small nuclear ribonucleoprotein PRP4 Chain: H
Molecule details ›
Chain: H
Length: 465 amino acids
Theoretical weight: 52.51 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20053 (Residues: 1-465; Coverage: 100%)
Gene names: P9705.6, PRP4, RNA4, YPR178W
Sequence domains: WD domain, G-beta repeat
Pre-mRNA-splicing factor 6 Chain: J
Molecule details ›
Chain: J
Length: 899 amino acids
Theoretical weight: 104.37 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P19735 (Residues: 1-899; Coverage: 100%)
Gene names: PRP6, RNA6, YBR0508, YBR055C
Sequence domains: PRP1 splicing factor, N-terminal
13 kDa ribonucleoprotein-associated protein Chain: K
Molecule details ›
Chain: K
Length: 126 amino acids
Theoretical weight: 13.58 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P39990 (Residues: 1-126; Coverage: 100%)
Gene names: SNU13, YEL026W
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
23 kDa U4/U6.U5 small nuclear ribonucleoprotein component Chain: L
Molecule details ›
Chain: L
Length: 194 amino acids
Theoretical weight: 22.72 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12368 (Residues: 1-194; Coverage: 100%)
Gene names: D2378, SNU23, YDL098C
Sequence domains: Zinc-finger of C2H2 type
Pre-mRNA-splicing factor 38 Chain: M
Molecule details ›
Chain: M
Length: 242 amino acids
Theoretical weight: 28 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q00723 (Residues: 1-242; Coverage: 100%)
Gene names: PRP38, YGR075C
Sequence domains: PRP38 family
Pre-mRNA-splicing factor SPP381 Chain: N
Molecule details ›
Chain: N
Length: 291 amino acids
Theoretical weight: 33.83 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38282 (Residues: 1-291; Coverage: 100%)
Gene names: SPP381, YBR1202, YBR152W
U2 snRNP component HSH155 Chain: O
Molecule details ›
Chain: O
Length: 971 amino acids
Theoretical weight: 110.17 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P49955 (Residues: 1-971; Coverage: 100%)
Gene names: HSH155, YM8021.14, YMR288W
Pre-mRNA-splicing factor RSE1 Chain: P
Molecule details ›
Chain: P
Length: 1361 amino acids
Theoretical weight: 153.96 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04693 (Residues: 1-1361; Coverage: 100%)
Gene names: RSE1, SAP130, YM9827.03C, YML049C
Sequence domains:
Cold sensitive U2 snRNA suppressor 1 Chain: Q
Molecule details ›
Chain: Q
Length: 435 amino acids
Theoretical weight: 50.21 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02554 (Residues: 1-435; Coverage: 100%)
Gene names: CUS1, YM9408.02C, YMR240C
Sequence domains:
Protein HSH49 Chain: R
Molecule details ›
Chain: R
Length: 213 amino acids
Theoretical weight: 24.53 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q99181 (Residues: 1-213; Coverage: 100%)
Gene names: HSH49, O6142, YOR319W
Sequence domains: RNA recognition motif
Pre-mRNA-splicing factor RDS3 Chain: S
Molecule details ›
Chain: S
Length: 107 amino acids
Theoretical weight: 12.28 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06835 (Residues: 1-107; Coverage: 100%)
Gene names: P9513.2, RDS3, YPR094W
Sequence domains: PHF5-like protein
Pre-mRNA-splicing factor PRP9 Chain: T
Molecule details ›
Chain: T
Length: 530 amino acids
Theoretical weight: 63.13 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P19736 (Residues: 1-530; Coverage: 100%)
Gene names: D2773, PRP9, YDL030W
Sequence domains:
Pre-mRNA-splicing factor PRP11 Chain: U
Molecule details ›
Chain: U
Length: 266 amino acids
Theoretical weight: 29.96 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q07350 (Residues: 1-266; Coverage: 100%)
Gene names: D2711, PRP10, PRP11, RNA11, YDL043C
Sequence domains:
Pre-mRNA-splicing factor PRP21 Chain: V
Molecule details ›
Chain: V
Length: 280 amino acids
Theoretical weight: 33.11 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32524 (Residues: 1-280; Coverage: 100%)
Gene names: J0322, PRP21, SPP91, YJL203W
Sequence domains:
U2 small nuclear ribonucleoprotein A' Chain: W
Molecule details ›
Chain: W
Length: 238 amino acids
Theoretical weight: 27.23 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q08963 (Residues: 1-238; Coverage: 100%)
Gene names: LEA1, YPL213W
Sequence domains: Leucine-rich repeat
Unknown Chain: X
Molecule details ›
Chain: X
Length: 111 amino acids
Theoretical weight: 7.91 KDa
Source organism: Saccharomyces cerevisiae
U2 small nuclear ribonucleoprotein B'' Chain: Y
Molecule details ›
Chain: Y
Length: 111 amino acids
Theoretical weight: 12.85 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40567 (Residues: 1-111; Coverage: 100%)
Gene names: MSL1, YIB9W, YIR009W
Sequence domains: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
RDS3 complex subunit 10 Chain: Z
Molecule details ›
Chain: Z
Length: 85 amino acids
Theoretical weight: 10.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C074 (Residues: 1-85; Coverage: 100%)
Gene names: RCP10, YNL138W-A, YSF3
Sequence domains: Splicing factor 3B subunit 10 (SF3b10)
U6 snRNA-associated Sm-like protein LSm2 Chain: a
Molecule details ›
Chain: a
Length: 95 amino acids
Theoretical weight: 11.18 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38203 (Residues: 1-95; Coverage: 100%)
Gene names: LSM2, SMX5, SNP3, YBL026W, YBL0425
Sequence domains: LSM domain
Small nuclear ribonucleoprotein-associated protein B Chains: b, k, s
Molecule details ›
Chains: b, k, s
Length: 196 amino acids
Theoretical weight: 22.43 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40018 (Residues: 1-196; Coverage: 100%)
Gene names: SMB1, YER029C
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D3 Chains: d, n, v
Molecule details ›
Chains: d, n, v
Length: 101 amino acids
Theoretical weight: 11.24 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P43321 (Residues: 1-101; Coverage: 100%)
Gene names: L9634.6, SMD3, YLR147C
Sequence domains: LSM domain
Small nuclear ribonucleoprotein E Chains: e, p, w
Molecule details ›
Chains: e, p, w
Length: 94 amino acids
Theoretical weight: 10.39 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12330 (Residues: 1-94; Coverage: 100%)
Gene names: SME1, YOR159C
Sequence domains: LSM domain
Small nuclear ribonucleoprotein F Chains: f, q, x
Molecule details ›
Chains: f, q, x
Length: 86 amino acids
Theoretical weight: 9.67 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P54999 (Residues: 1-86; Coverage: 100%)
Gene names: P9705.4, SMX3, YPR182W
Sequence domains: LSM domain
Small nuclear ribonucleoprotein G Chains: g, r, y
Molecule details ›
Chains: g, r, y
Length: 77 amino acids
Theoretical weight: 8.49 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40204 (Residues: 1-77; Coverage: 100%)
Gene names: SMX2, SNP2, YFL017Bw, YFL017W-A
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D1 Chains: h, l, t
Molecule details ›
Chains: h, l, t
Length: 146 amino acids
Theoretical weight: 16.3 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02260 (Residues: 1-146; Coverage: 100%)
Gene names: SMD1, YGR074W
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D2 Chains: i, m, u
Molecule details ›
Chains: i, m, u
Length: 110 amino acids
Theoretical weight: 12.88 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06217 (Residues: 1-110; Coverage: 100%)
Gene names: L9328.5, SMD2, YLR275W
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm4 Chain: j
Molecule details ›
Chain: j
Length: 187 amino acids
Theoretical weight: 21.3 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40070 (Residues: 1-187; Coverage: 100%)
Gene names: LSM4, SDB23, USS1, YER112W
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm5 Chain: o
Molecule details ›
Chain: o
Length: 93 amino acids
Theoretical weight: 10.43 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40089 (Residues: 1-93; Coverage: 100%)
Gene names: LSM5, YER146W
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm6 Chain: z
Molecule details ›
Chain: z
Length: 86 amino acids
Theoretical weight: 9.41 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: A6ZYX7 (Residues: 1-86; Coverage: 100%)
Gene names: LSM6, SCY_1265
Sequence domains: LSM domain
U2 snRNA Chain: 2
Molecule details ›
Chain: 2
Length: 1175 nucleotides
Theoretical weight: 376.27 KDa
Sequence domains: U2 spliceosomal RNA
U4 snRNA Chain: 4
Molecule details ›
Chain: 4
Length: 160 nucleotides
Theoretical weight: 51.19 KDa
Sequence domains: U4 spliceosomal RNA
U5 snRNA Chain: 5
Molecule details ›
Chain: 5
Length: 214 nucleotides
Theoretical weight: 68.64 KDa
Sequence domains: U5 spliceosomal RNA
U6 snRNA Chain: 6
Molecule details ›
Chain: 6
Length: 112 nucleotides
Theoretical weight: 35.88 KDa
Sequence domains: U6 spliceosomal RNA
Yeast UBC4 gene for ubiquitin-conjugating enzyme Chain: I
Molecule details ›
Chain: I
Length: 95 nucleotides
Theoretical weight: 30.2 KDa

Ligands and Environments

2 bound ligands:
Ligand GTP 1 x GTP
Ligand ZN 7 x ZN
1 modified residue:
Ligand PSU 3 x PSU

Experiments and Validation Details

Entry percentile scores
Resolution: 7.2Å
Relevant EMDB volumes: EMD-3683

Quick links

Citations

33 review citations

A brave new world of RNA-binding proteins.
Hentze et al. (2018)
32 more

20 mentions without citation

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine.
Fica et al. (2017)
19 more