› 7qtt

Electron Microscopy
3.1Å resolution

Structural organization of a late activated human spliceosome (Baqr, core region)

Released:
DOI: 10.2210/pdb7qtt/pdb
PDB entry 7qtt coloured by chain, front view.
PDB entry 7qtt coloured by chain, side view.
PDB entry 7qtt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of catalytic activation in human splicing.
Schmitzová J, Cretu C, Dienemann C, Urlaub H, Pena V
OpenAccess logo Nature (2023)
PMID: 37165190
Related structures: EMD-14146

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
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 37-mer (preferred)
PDBe Complex ID:
PDB-CPX-216243 (preferred)
Entry contents:
33 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (37 distinct):
Splicing factor 3B subunit 3 Chain: A
Molecule details ›
Chain: A
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: B
Molecule details ›
Chain: B
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)
Splicing factor 3B subunit 1 Chain: C
Molecule details ›
Chain: C
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:
PHD finger-like domain-containing protein 5A Chain: D
Molecule details ›
Chain: D
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 2 Chain: E
Molecule details ›
Chain: E
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 4 Chain: F
Molecule details ›
Chain: F
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
G-patch domain and KOW motifs-containing protein Chain: G
Molecule details ›
Chain: G
Length: 476 amino acids
Theoretical weight: 52.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q92917 (Residues: 1-476; Coverage: 100%)
Gene names: GPATC5, GPATCH5, GPKOW, T54
Sequence domains:
Splicing factor 3A subunit 2 Chain: I
Molecule details ›
Chain: I
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 3A subunit 3 Chain: J
Molecule details ›
Chain: J
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:
BUD13 homolog Chain: L
Molecule details ›
Chain: L
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: N
Molecule details ›
Chain: N
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:
Pleiotropic regulator 1 Chain: O
Molecule details ›
Chain: O
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
Cell division cycle 5-like protein Chain: P
Molecule details ›
Chain: P
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:
Spliceosome-associated protein CWC15 homolog Chain: Q
Molecule details ›
Chain: Q
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
Protein BUD31 homolog Chain: T
Molecule details ›
Chain: T
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: U
Molecule details ›
Chain: U
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:
Peptidyl-prolyl cis-trans isomerase-like 4 Chain: V
Molecule details ›
Chain: V
Length: 492 amino acids
Theoretical weight: 57.32 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8WUA2 (Residues: 1-492; Coverage: 100%)
Gene name: PPIL4
Sequence domains:
Pre-mRNA-splicing factor CWC22 homolog Chain: W
Molecule details ›
Chain: W
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:
Crooked neck-like protein 1 Chain: X
Molecule details ›
Chain: X
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
SNW domain-containing protein 1 Chain: Y
Molecule details ›
Chain: Y
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
E3 ubiquitin-protein ligase RNF113A Chain: Z
Molecule details ›
Chain: Z
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:
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:
Small nuclear ribonucleoprotein F Chain: h
Molecule details ›
Chain: h
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 Chain: i
Molecule details ›
Chain: i
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 Sm D3 Chain: j
Molecule details ›
Chain: j
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 Sm D1 Chain: k
Molecule details ›
Chain: k
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 Chain: l
Molecule details ›
Chain: l
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 G Chain: m
Molecule details ›
Chain: m
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-associated proteins B and B' Chain: n
Molecule details ›
Chain: n
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
Peptidyl-prolyl cis-trans isomerase-like 1 Chain: p
Molecule details ›
Chain: p
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
Serine/arginine repetitive matrix protein 2 Chain: q
Molecule details ›
Chain: q
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
RING-type E3 ubiquitin-protein ligase PPIL2 Chain: u
Molecule details ›
Chain: u
Length: 520 amino acids
Theoretical weight: 58.91 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13356 (Residues: 1-520; Coverage: 100%)
Gene name: PPIL2
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
U6snRNA Chain: d
Molecule details ›
Chain: d
Length: 106 nucleotides
Theoretical weight: 34.1 KDa
Sequence domains: U6 spliceosomal RNA
U5 snRNA Chain: e
Molecule details ›
Chain: e
Length: 117 nucleotides
Theoretical weight: 37.25 KDa
Sequence domains: U5 spliceosomal RNA
U2snRNA Chain: f
Molecule details ›
Chain: f
Length: 188 nucleotides
Theoretical weight: 60.19 KDa
Sequence domains: U2 spliceosomal RNA
MINX Chain: g
Molecule details ›
Chain: g
Length: 319 nucleotides
Theoretical weight: 102.35 KDa

Ligands and Environments

4 bound ligands:
Ligand ZN 12 x ZN
Ligand IHP 1 x IHP
Ligand GTP 1 x GTP
Ligand MG 7 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-14146

Quick links

Citations

2 review citations

Pre-mRNA splicing-associated diseases and therapies.
Love et al. (2023)
1 more