› 6ff4

Electron Microscopy
3.4Å resolution

human Bact spliceosome core structure

Released:
DOI: 10.2210/pdb6ff4/pdb
PDB entry 6ff4 coloured by chain, front view.
PDB entry 6ff4 coloured by chain, side view.
PDB entry 6ff4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure and Conformational Dynamics of the Human Spliceosomal Bact Complex.
Haselbach D, Komarov I, Agafonov DE, Hartmuth K, Graf B, Dybkov O, Urlaub H, Kastner B, Lührmann R, Stark H
Cell 172 454-464.e11 (2018)
PMID: 29361316
Related structures: EMD-4255

Function and Biology Details

Reactions catalysed: 
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 28-mer (preferred)
PDBe Complex ID:
PDB-CPX-127529 (preferred)
Entry contents:
24 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (28 distinct):
RNA-binding motif protein, X-linked 2 Chain: 1
Molecule details ›
Chain: 1
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: 3
Molecule details ›
Chain: 3
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
Splicing factor 3A subunit 2 Chain: 7
Molecule details ›
Chain: 7
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 2 Chain: 8
Molecule details ›
Chain: 8
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:
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:
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
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: 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:
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
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
Structure domains: Cyclophilin-like
Serine/arginine repetitive matrix protein 1 Chain: Y
Molecule details ›
Chain: Y
Length: 904 amino acids
Theoretical weight: 102.6 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8IYB3 (Residues: 1-904; Coverage: 100%)
Gene names: SRM160, SRRM1
Sequence domains: PWI domain
Structure domains: PWI domain
Spliceosome-associated protein CWC27 homolog Chain: s
Molecule details ›
Chain: s
Length: 472 amino acids
Theoretical weight: 53.94 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6UX04 (Residues: 1-472; Coverage: 100%)
Gene names: CWC27, SDCCAG10, UNQ438/PRO871
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
Structure domains: Cyclophilin-like
E3 ubiquitin-protein ligase RNF113A Chain: t
Molecule details ›
Chain: t
Length: 343 amino acids
Theoretical weight: 38.85 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15541 (Residues: 1-343; Coverage: 100%)
Gene names: RNF113, RNF113A, ZNF183
Sequence domains:
Splicing factor 3B subunit 1 Chain: u
Molecule details ›
Chain: u
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: v
Molecule details ›
Chain: v
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
Splicing factor 3B subunit 6 Chain: z
Molecule details ›
Chain: z
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
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: 107 nucleotides
Theoretical weight: 34.4 KDa
Sequence domains: U6 spliceosomal RNA
pre mRNA Chain: Z
Molecule details ›
Chain: Z
Length: 478 nucleotides
Theoretical weight: 153.79 KDa

Ligands and Environments

4 bound ligands:
Ligand MG 4 x MG
Ligand IHP 1 x IHP
Ligand GTP 1 x GTP
Ligand ZN 10 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.4Å
Relevant EMDB volumes: EMD-4255

Quick links

Citations

28 review citations

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

11 mentions without citation

Structures of SF3b1 reveal a dynamic Achilles heel of spliceosome assembly: Implications for cancer-associated abnormalities and drug discovery.
Maji et al. (2019)
10 more