› 7abg

Electron Microscopy
7.8Å resolution

Human pre-Bact-1 spliceosome

Released:
DOI: 10.2210/pdb7abg/pdb
PDB entry 7abg coloured by chain, front view.
PDB entry 7abg coloured by chain, side view.
PDB entry 7abg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation.
Townsend C, Leelaram MN, Agafonov DE, Dybkov O, Will CL, Bertram K, Urlaub H, Kastner B, Stark H, Lührmann R
Science 370 (2020)
PMID: 33243851
Related structures: EMD-11695

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 58-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127125 (preferred)
Entry contents:
47 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (51 distinct):
Nuclear cap-binding protein subunit 1 Chain: A5
Molecule details ›
Chain: A5
Length: 790 amino acids
Theoretical weight: 91.96 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q09161 (Residues: 1-790; Coverage: 100%)
Gene names: CBP80, NCBP, NCBP1
Sequence domains:
U6 snRNA-associated Sm-like protein LSm7 Chain: A2
Molecule details ›
Chain: A2
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
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
Splicing factor 3A subunit 2 Chain: F
Molecule details ›
Chain: F
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:
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
U2 small nuclear ribonucleoprotein A' Chain: W
Molecule details ›
Chain: W
Length: 255 amino acids
Theoretical weight: 28.46 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P09661 (Residues: 1-255; Coverage: 100%)
Gene name: SNRPA1
Sequence domains: Leucine-rich repeat
U2 small nuclear ribonucleoprotein B'' Chain: B
Molecule details ›
Chain: B
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
U5 small nuclear ribonucleoprotein 200 kDa helicase Chain: s
Molecule details ›
Chain: s
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:
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
Nuclear cap-binding protein subunit 2 Chain: A1
Molecule details ›
Chain: A1
Length: 156 amino acids
Theoretical weight: 18.03 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P52298 (Residues: 1-156; Coverage: 100%)
Gene names: CBP20, NCBP2, PIG55
Sequence domains: RNA recognition motif
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:
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
U6 snRNA-associated Sm-like protein LSm2 Chain: V
Molecule details ›
Chain: V
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: 9
Molecule details ›
Chain: 9
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: C
Molecule details ›
Chain: C
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: H
Molecule details ›
Chain: H
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: J
Molecule details ›
Chain: J
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 LSm8 Chain: A3
Molecule details ›
Chain: A3
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
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
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
Pleiotropic regulator 1 Chain: G
Molecule details ›
Chain: G
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-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:
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:
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:
Splicing factor 3A subunit 1 Chain: p
Molecule details ›
Chain: p
Length: 793 amino acids
Theoretical weight: 88.99 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15459 (Residues: 1-793; Coverage: 100%)
Gene names: SAP114, SF3A1
Sequence domains:
Splicing factor 3A subunit 3 Chain: 4
Molecule details ›
Chain: 4
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:
Transcription elongation regulator 1 Chain: A4
Molecule details ›
Chain: A4
Length: 1098 amino acids
Theoretical weight: 124.08 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O14776 (Residues: 1-1098; Coverage: 100%)
Gene names: CA150, TAF2S, TCERG1
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 2 Chain: T
Molecule details ›
Chain: T
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: E
Molecule details ›
Chain: E
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 4 Chain: w
Molecule details ›
Chain: w
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 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)
SNW domain-containing protein 1 Chain: v
Molecule details ›
Chain: v
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
Smad nuclear-interacting protein 1 Chain: 0
Molecule details ›
Chain: 0
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
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
116 kDa U5 small nuclear ribonucleoprotein component Chain: r
Molecule details ›
Chain: r
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:
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
Serine/arginine-rich splicing factor 1 Chain: A6
Molecule details ›
Chain: A6
Length: 248 amino acids
Theoretical weight: 27.8 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q07955 (Residues: 1-248; Coverage: 100%)
Gene names: ASF, OK/SW-cl.3, SF2, SF2P33, SFRS1, SRSF1
Sequence domains: RNA recognition motif
Small nuclear ribonucleoprotein Sm D2 Chains: a, h
Molecule details ›
Chains: 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: b, i
Molecule details ›
Chains: 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-associated proteins B and B' Chains: f, m
Molecule details ›
Chains: 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 D3 Chains: e, l
Molecule details ›
Chains: 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 G Chains: d, k
Molecule details ›
Chains: 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 E Chains: c, j
Molecule details ›
Chains: 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 Sm D1 Chains: g, n
Molecule details ›
Chains: 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
Ubiquitin-like protein 5 Chain: q
Molecule details ›
Chain: q
Length: 73 amino acids
Theoretical weight: 8.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BZL1 (Residues: 1-73; Coverage: 100%)
Gene name: UBL5
Sequence domains: Ubiquitin family
WW domain-binding protein 11 Chain: X
Molecule details ›
Chain: X
Length: 641 amino acids
Theoretical weight: 70.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y2W2 (Residues: 1-641; Coverage: 100%)
Gene names: NPWBP, SIPP1, SNP70, WBP11
Sequence domains: WW domain binding protein 11
U5 snRNA Chain: 5
Molecule details ›
Chain: 5
Length: 116 nucleotides
Theoretical weight: 36.91 KDa
Sequence domains: U5 spliceosomal RNA
U2 snRNA Chain: 2
Molecule details ›
Chain: 2
Length: 188 nucleotides
Theoretical weight: 60.19 KDa
Sequence domains: U2 spliceosomal RNA
MINX M3 pre-mRNA Chain: Z
Molecule details ›
Chain: Z
Length: 230 nucleotides
Theoretical weight: 73.71 KDa
U6 snRNA Chain: 6
Molecule details ›
Chain: 6
Length: 106 nucleotides
Theoretical weight: 34.1 KDa
Sequence domains: U6 spliceosomal RNA

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 7.8Å
Relevant EMDB volumes: EMD-11695

Quick links

Citations

8 review citations

Biology of the mRNA Splicing Machinery and Its Dysregulation in Cancer Providing Therapeutic Opportunities.
Blijlevens et al. (2021)
7 more

2 mentions without citation

UBL5/Hub1: An Atypical Ubiquitin-Like Protein with a Typical Role as a Stress-Responsive Regulator.
Chanarat S. (2021)
1 more