› 5o9z

Electron Microscopy
4.5Å resolution

Cryo-EM structure of a pre-catalytic human spliceosome primed for activation (B complex)

Released:
DOI: 10.2210/pdb5o9z/pdb
PDB entry 5o9z coloured by chain, front view.
PDB entry 5o9z coloured by chain, side view.
PDB entry 5o9z coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation.
Bertram K, Agafonov DE, Dybkov O, Haselbach D, Leelaram MN, Will CL, Urlaub H, Kastner B, Lührmann R, Stark H
Cell 170 701-713.e11 (2017)
PMID: 28781166
Related structures: EMD-3766

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
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-128856 (preferred)
Entry contents:
38 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (43 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: B
Molecule details ›
Chain: B
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: C
Molecule details ›
Chain: C
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: D
Molecule details ›
Chain: D
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
U4/U6 small nuclear ribonucleoprotein Prp3 Chain: E
Molecule details ›
Chain: E
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:
U4/U6 small nuclear ribonucleoprotein Prp4 Chain: F
Molecule details ›
Chain: F
Length: 521 amino acids
Theoretical weight: 58.41 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43172 (Residues: 1-522; Coverage: 100%)
Gene names: PRP4, PRPF4
Sequence domains:
Pre-mRNA-processing factor 6 Chain: G
Molecule details ›
Chain: G
Length: 941 amino acids
Theoretical weight: 107.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O94906 (Residues: 1-941; Coverage: 100%)
Gene names: C20orf14, PRPF6
Sequence domains:
U4/U6 small nuclear ribonucleoprotein Prp31 Chain: H
Molecule details ›
Chain: H
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:
Pre-mRNA-splicing factor 38A Chain: I
Molecule details ›
Chain: I
Length: 312 amino acids
Theoretical weight: 37.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8NAV1 (Residues: 1-312; Coverage: 100%)
Gene name: PRPF38A
Sequence domains:
Thioredoxin-like protein 4A Chain: J
Molecule details ›
Chain: J
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
Microfibrillar-associated protein 1 Chain: K
Molecule details ›
Chain: K
Length: 439 amino acids
Theoretical weight: 52.05 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P55081 (Residues: 1-439; Coverage: 100%)
Gene name: MFAP1
Sequence domains: Microfibril-associated/Pre-mRNA processing
WD40 repeat-containing protein SMU1 Chain: L
Molecule details ›
Chain: L
Length: 513 amino acids
Theoretical weight: 57.62 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q2TAY7 (Residues: 1-513; Coverage: 100%)
Gene name: SMU1
Sequence domains:
Peptidyl-prolyl cis-trans isomerase H Chain: M
Molecule details ›
Chain: M
Length: 177 amino acids
Theoretical weight: 19.23 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43447 (Residues: 1-177; Coverage: 100%)
Gene names: CYP20, CYPH, PPIH
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
Zinc finger matrin-type protein 2 Chain: N
Molecule details ›
Chain: N
Length: 199 amino acids
Theoretical weight: 23.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96NC0 (Residues: 1-199; Coverage: 100%)
Gene name: ZMAT2
Sequence domains: Zinc-finger double-stranded RNA-binding
NHP2-like protein 1 Chain: O
Molecule details ›
Chain: O
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
U4/U6.U5 tri-snRNP-associated protein 1 Chain: P
Molecule details ›
Chain: P
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:
WW domain-binding protein 4 Chain: Q
Molecule details ›
Chain: Q
Length: 376 amino acids
Theoretical weight: 42.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75554 (Residues: 1-376; Coverage: 100%)
Gene names: FBP21, FNBP21, WBP4
Sequence domains:
Protein Red Chain: R
Molecule details ›
Chain: R
Length: 557 amino acids
Theoretical weight: 65.73 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13123 (Residues: 1-557; Coverage: 100%)
Gene names: IK, RED, RER
Sequence domains:
Small nuclear ribonucleoprotein Sm D2 Chains: S, a, h
Molecule details ›
Chains: S, a, h
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: T, b, i
Molecule details ›
Chains: T, b, i
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: U, c, j
Molecule details ›
Chains: U, c, j
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: V, d, k
Molecule details ›
Chains: V, d, k
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
Small nuclear ribonucleoprotein Sm D3 Chains: W, e, l
Molecule details ›
Chains: W, e, l
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: X, f, m
Molecule details ›
Chains: X, f, m
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
Small nuclear ribonucleoprotein Sm D1 Chains: Z, g, n
Molecule details ›
Chains: Z, g, n
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
U6 snRNA-associated Sm-like protein LSm2 Chain: o
Molecule details ›
Chain: o
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
U6 snRNA-associated Sm-like protein LSm3 Chain: p
Molecule details ›
Chain: p
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
U6 snRNA-associated Sm-like protein LSm4 Chain: q
Molecule details ›
Chain: q
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
U6 snRNA-associated Sm-like protein LSm5 Chain: r
Molecule details ›
Chain: r
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
U6 snRNA-associated Sm-like protein LSm6 Chain: s
Molecule details ›
Chain: s
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
U6 snRNA-associated Sm-like protein LSm7 Chain: t
Molecule details ›
Chain: t
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 LSm8 Chain: u
Molecule details ›
Chain: u
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
Splicing factor 3B subunit 1 Chain: v
Molecule details ›
Chain: v
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 3 Chain: w
Molecule details ›
Chain: w
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 5 Chain: x
Molecule details ›
Chain: x
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)
PHD finger-like domain-containing protein 5A Chain: y
Molecule details ›
Chain: y
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
U2 small nuclear ribonucleoprotein A' Chain: z
Molecule details ›
Chain: z
Length: 256 amino acids
Theoretical weight: 28.63 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P09661 (Residues: 1-151, 153-255; Coverage: 100%)
Gene name: SNRPA1
Sequence domains: Leucine-rich repeat
U2 small nuclear ribonucleoprotein B'' Chain: 1
Molecule details ›
Chain: 1
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
MINX pre-mRNA Chain: Y
Molecule details ›
Chain: Y
Length: 324 nucleotides
Theoretical weight: 103.98 KDa
Human gene for small nuclear RNA U2 (snRNA U2) Chain: 2
Molecule details ›
Chain: 2
Length: 188 nucleotides
Theoretical weight: 60.19 KDa
Sequence domains: U2 spliceosomal RNA
Homo sapiens U4A snRNA Chain: 4
Molecule details ›
Chain: 4
Length: 145 nucleotides
Theoretical weight: 46.53 KDa
Sequence domains: U4 spliceosomal RNA
Homo sapiens U5 A small nuclear RNA Chain: 5
Molecule details ›
Chain: 5
Length: 116 nucleotides
Theoretical weight: 36.91 KDa
Sequence domains: U5 spliceosomal RNA
Homo sapiens RNA, U6 small nuclear 1 (RNU6-1), small nuclear RNA Chain: 6
Molecule details ›
Chain: 6
Length: 106 nucleotides
Theoretical weight: 34.1 KDa
Sequence domains: U6 spliceosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.5Å
Relevant EMDB volumes: EMD-3766

Quick links

Citations

29 review citations

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

13 mentions without citation

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