› 7dvq

Electron Microscopy
2.89Å resolution

Cryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex)

Released:
DOI: 10.2210/pdb7dvq/pdb
PDB entry 7dvq coloured by chain, front view.
PDB entry 7dvq coloured by chain, side view.
PDB entry 7dvq coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of the activated human minor spliceosome.
Bai R, Wan R, Wang L, Xu K, Zhang Q, Lei J, Shi Y
Science 371 (2021)
PMID: 33509932
Related structures: EMD-30875

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 49-mer (preferred)
PDBe Complex ID:
PDB-CPX-249700 (preferred)
Entry contents:
38 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (42 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: C
Molecule details ›
Chain: C
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: D
Molecule details ›
Chain: D
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: E
Molecule details ›
Chain: E
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
Small nuclear ribonucleoprotein Sm D3 Chains: a, h
Molecule details ›
Chains: a, h
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: b, i
Molecule details ›
Chains: b, i
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: c, j
Molecule details ›
Chains: c, j
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 Chains: d, k
Molecule details ›
Chains: d, k
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: f, m
Molecule details ›
Chains: f, m
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: e, l
Molecule details ›
Chains: e, l
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: g, n
Molecule details ›
Chains: g, n
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
Sodium channel modifier 1 Chain: v
Molecule details ›
Chain: v
Length: 230 amino acids
Theoretical weight: 25.99 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BWG6 (Residues: 1-230; Coverage: 100%)
Gene name: SCNM1
Sequence domains:
Splicing factor 3B subunit 1 Chain: 1
Molecule details ›
Chain: 1
Length: 1304 amino acids
Theoretical weight: 146.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75533 (Residues: 1-1304; Coverage: 100%)
Gene names: SAP155, SF3B1
Sequence domains:
Splicing factor 3B subunit 2 Chain: 2
Molecule details ›
Chain: 2
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 3 Chain: 3
Molecule details ›
Chain: 3
Length: 1217 amino acids
Theoretical weight: 135.8 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15393 (Residues: 1-1217; Coverage: 100%)
Gene names: KIAA0017, SAP130, SF3B3
Sequence domains:
Splicing factor 3B subunit 4 Chain: 4
Molecule details ›
Chain: 4
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
Splicing factor 3B subunit 6 Chain: 5
Molecule details ›
Chain: 5
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
PHD finger-like domain-containing protein 5A Chain: 6
Molecule details ›
Chain: 6
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 5 Chain: 7
Molecule details ›
Chain: 7
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)
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: J
Molecule details ›
Chain: J
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
Spliceosome-associated protein CWC15 homolog Chain: P
Molecule details ›
Chain: P
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
SNW domain-containing protein 1 Chain: R
Molecule details ›
Chain: R
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: T
Molecule details ›
Chain: T
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
Smad nuclear-interacting protein 1 Chain: X
Molecule details ›
Chain: X
Length: 396 amino acids
Theoretical weight: 45.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8TAD8 (Residues: 1-396; Coverage: 100%)
Gene name: SNIP1
Sequence domains: FHA domain
RNA-binding motif protein, X-linked 2 Chain: Y
Molecule details ›
Chain: Y
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: Z
Molecule details ›
Chain: Z
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
RING-type E3 ubiquitin-protein ligase PPIL2 Chain: 9
Molecule details ›
Chain: 9
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
Spliceosome-associated protein CWC27 homolog Chain: z
Molecule details ›
Chain: z
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
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 Chain: x
Molecule details ›
Chain: x
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:
G-patch domain and KOW motifs-containing protein Chain: y
Molecule details ›
Chain: y
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:
E3 ubiquitin-protein ligase RNF113A Chain: M
Molecule details ›
Chain: M
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:
Serine/arginine repetitive matrix protein 2 Chain: U
Molecule details ›
Chain: U
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: V
Molecule details ›
Chain: V
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:
Serine/arginine repetitive matrix protein 1 Chain: 8
Molecule details ›
Chain: 8
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
Cysteine-rich PDZ-binding protein Chain: 0
Molecule details ›
Chain: 0
Length: 101 amino acids
Theoretical weight: 11.24 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9P021 (Residues: 1-101; Coverage: 100%)
Gene names: CRIPT, HSPC139
Sequence domains: Microtubule-associated protein CRIPT
RNA-binding protein 48 Chain: I
Molecule details ›
Chain: I
Length: 367 amino acids
Theoretical weight: 41.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q5RL73 (Residues: 1-367; Coverage: 100%)
Gene names: C7orf64, HSPC304, RBM48
Armadillo repeat-containing protein 7 Chain: K
Molecule details ›
Chain: K
Length: 198 amino acids
Theoretical weight: 21.95 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9H6L4 (Residues: 1-198; Coverage: 100%)
Gene name: ARMC7
Sequence domains: Armadillo/beta-catenin-like repeat
U5 snRNA Chain: B
Molecule details ›
Chain: B
Length: 117 nucleotides
Theoretical weight: 37.25 KDa
Sequence domains: U5 spliceosomal RNA
U6atac snRNA Chain: F
Molecule details ›
Chain: F
Length: 124 nucleotides
Theoretical weight: 39.88 KDa
Sequence domains: U6atac minor spliceosomal RNA
pre-mRNA Chain: G
Molecule details ›
Chain: G
Length: 142 nucleotides
Theoretical weight: 44.32 KDa
U12 snRNA Chain: H
Molecule details ›
Chain: H
Length: 150 nucleotides
Theoretical weight: 48.35 KDa
Sequence domains: U12 minor spliceosomal RNA

Ligands and Environments

6 bound ligands:
Ligand IHP 1 x IHP
Ligand GTP 1 x GTP
Ligand MG 5 x MG
Ligand K 2 x K
Ligand G5J 1 x G5J
Ligand ZN 7 x ZN
2 modified residues:
Ligand SEP 1 x SEP
Ligand TPO 1 x TPO

Experiments and Validation Details

Entry percentile scores
Resolution: 2.89Å
Relevant EMDB volumes: EMD-30875

Quick links

Citations

5 review citations

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