› 6zym

Electron Microscopy
3.4Å resolution

Human C Complex Spliceosome - High-resolution CORE

Released:
DOI: 10.2210/pdb6zym/pdb
PDB entry 6zym coloured by chain, front view.
PDB entry 6zym coloured by chain, side view.
PDB entry 6zym coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Insights into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome.
Bertram K, El Ayoubi L, Dybkov O, Agafonov DE, Will CL, Hartmuth K, Urlaub H, Kastner B, Stark H, Lührmann R
Mol Cell 80 127-139.e6 (2020)
PMID: 33007253
Related structures: EMD-11569

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 26-mer (preferred)
PDBe Complex ID:
PDB-CPX-129053 (preferred)
Entry contents:
21 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (25 distinct):
Corepressor interacting with RBPJ 1 Chain: 9
Molecule details ›
Chain: 9
Length: 450 amino acids
Theoretical weight: 52.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q86X95 (Residues: 1-450; Coverage: 100%)
Gene names: CIR, CIR1
Sequence domains: N-terminal domain of CBF1 interacting co-repressor CIR
Pre-mRNA-processing-splicing factor 8 Chain: A
Molecule details ›
Chain: A
Length: 1755 amino acids
Theoretical weight: 207.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6P2Q9 (Residues: 1-1755; Coverage: 75%)
Gene names: PRPC8, PRPF8
Sequence domains:
116 kDa U5 small nuclear ribonucleoprotein component Chain: B
Molecule details ›
Chain: B
Length: 952 amino acids
Theoretical weight: 107.23 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15029 (Residues: 1-952; Coverage: 98%)
Gene names: EFTUD2, KIAA0031, SNRP116
Sequence domains:
SNW domain-containing protein 1 Chain: C
Molecule details ›
Chain: C
Length: 536 amino acids
Theoretical weight: 61.61 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13573 (Residues: 1-536; Coverage: 100%)
Gene names: SKIIP, SKIP, SNW1
Sequence domains: SKIP/SNW domain
Pleiotropic regulator 1 Chain: D
Molecule details ›
Chain: D
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
Pre-mRNA-processing factor 17 Chain: E
Molecule details ›
Chain: E
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
U5 small nuclear ribonucleoprotein 40 kDa protein Chain: F
Molecule details ›
Chain: F
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
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:
Crooked neck-like protein 1 Chain: O
Molecule details ›
Chain: O
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 RBM22 Chain: P
Molecule details ›
Chain: P
Length: 218 amino acids
Theoretical weight: 25.22 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NW64 (Residues: 1-218; Coverage: 52%)
Gene names: 199G4, RBM22, ZC3H16
Sequence domains: STL11, N-terminal
Protein BUD31 homolog Chain: Q
Molecule details ›
Chain: Q
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
Spliceosome-associated protein CWC15 homolog Chain: R
Molecule details ›
Chain: R
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: S
Molecule details ›
Chain: S
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: T
Molecule details ›
Chain: T
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:
Peptidyl-prolyl cis-trans isomerase-like 1 Chain: V
Molecule details ›
Chain: V
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
WD repeat-containing protein 70 Chain: p
Molecule details ›
Chain: p
Length: 654 amino acids
Theoretical weight: 73.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NW82 (Residues: 1-654; Coverage: 100%)
Gene name: WDR70
Sequence domains: WD domain, G-beta repeat
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 Chain: r
Molecule details ›
Chain: r
Length: 1227 amino acids
Theoretical weight: 140.72 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q92620 (Residues: 1-1227; Coverage: 100%)
Gene names: DDX38, DHX38, KIAA0224, PRP16
Sequence domains:
Pre-mRNA-splicing factor ISY1 homolog Chain: s
Molecule details ›
Chain: s
Length: 285 amino acids
Theoretical weight: 33.05 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9ULR0 (Residues: 1-285; Coverage: 100%)
Gene names: ISY1, KIAA1160
Sequence domains: Isy1-like splicing family
Pre-mRNA-splicing factor CWC25 homolog Chain: t
Molecule details ›
Chain: t
Length: 425 amino acids
Theoretical weight: 49.77 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NXE8 (Residues: 1-425; Coverage: 100%)
Gene names: CCDC49, CWC25
Sequence domains:
Splicing factor YJU2 Chain: u
Molecule details ›
Chain: u
Length: 178 amino acids
Theoretical weight: 21.45 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BW85 (Residues: 1-178; Coverage: 55%)
Gene names: CCDC94, YJU2
Sequence domains: Saf4/Yju2 protein
Protein FRG1 Chain: x
Molecule details ›
Chain: x
Length: 258 amino acids
Theoretical weight: 29.23 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q14331 (Residues: 1-258; Coverage: 100%)
Gene name: FRG1
Sequence domains: FRG1-like domain
U2 snRNA Chain: 2
Molecule details ›
Chain: 2
Length: 188 nucleotides
Theoretical weight: 60.19 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: 79 nucleotides
Theoretical weight: 25.48 KDa
Sequence domains: U6 spliceosomal RNA
pre-mRNA Chains: Y, Z
Molecule details ›
Chains: Y, Z
Length: 324 nucleotides
Theoretical weight: 103.98 KDa

Ligands and Environments

4 bound ligands:
Ligand MG 5 x MG
Ligand IHP 1 x IHP
Ligand GTP 1 x GTP
Ligand ZN 7 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.4Å
Relevant EMDB volumes: EMD-11569

Quick links

Citations

5 review citations

Recent advances and current trends in cryo-electron microscopy.
Guaita et al. (2022)
4 more

5 mentions without citation

Structural basis for conformational equilibrium of the catalytic spliceosome.
Wilkinson et al. (2021)
4 more