› 8h6e

Electron Microscopy
3.2Å resolution

Cryo-EM structure of human exon-defined spliceosome in the late pre-B state.

Released:
DOI: 10.2210/pdb8h6e/pdb
PDB entry 8h6e coloured by chain, front view.
PDB entry 8h6e coloured by chain, side view.
PDB entry 8h6e coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into human exon-defined spliceosome prior to activation.
Zhang W, Zhang X, Zhan X, Bai R, Lei J, Yan C, Shi Y
OpenAccess logo Cell Res (2024)
PMID: 38658629
Related structures: EMD-34500

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 61-mer (preferred)
PDBe Complex ID:
PDB-CPX-271698 (preferred)
Entry contents:
42 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (47 distinct):
U6 snRNA-associated Sm-like protein LSm2 Chain: 6a
Molecule details ›
Chain: 6a
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: 6b
Molecule details ›
Chain: 6b
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: 6c
Molecule details ›
Chain: 6c
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: 6d
Molecule details ›
Chain: 6d
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: 6e
Molecule details ›
Chain: 6e
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 LSm7 Chain: 6f
Molecule details ›
Chain: 6f
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
U6 snRNA-associated Sm-like protein LSm8 Chain: 6g
Molecule details ›
Chain: 6g
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
Pre-mRNA-processing-splicing factor 8 Chain: 5B
Molecule details ›
Chain: 5B
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: 5C
Molecule details ›
Chain: 5C
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: 5D
Molecule details ›
Chain: 5D
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: 5E
Molecule details ›
Chain: 5E
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-associated proteins B and B' Chains: 2a, 4a, 5a
Molecule details ›
Chains: 2a, 4a, 5a
Length: 231 amino acids
Theoretical weight: 23.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P14678 (Residues: 1-229; Coverage: 95%)
  • Best match: P14678-2 (Residues: 1-231)
Gene names: COD, SNRPB, SNRPB1
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D1 Chains: 2b, 4b, 5b
Molecule details ›
Chains: 2b, 4b, 5b
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: 2c, 4c, 5c
Molecule details ›
Chains: 2c, 4c, 5c
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: 2d, 4d, 5d
Molecule details ›
Chains: 2d, 4d, 5d
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: 2e, 4e, 5e
Molecule details ›
Chains: 2e, 4e, 5e
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: 2f, 4f, 5f
Molecule details ›
Chains: 2f, 4f, 5f
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 Sm D3 Chains: 2g, 4g, 5g
Molecule details ›
Chains: 2g, 4g, 5g
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
U4/U6 small nuclear ribonucleoprotein Prp3 Chain: 4B
Molecule details ›
Chain: 4B
Length: 683 amino acids
Theoretical weight: 77.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43395 (Residues: 1-683; Coverage: 100%)
Gene names: HPRP3, PRP3, PRPF3
Sequence domains:
U4/U6 small nuclear ribonucleoprotein Prp4 Chain: 4C
Molecule details ›
Chain: 4C
Length: 522 amino acids
Theoretical weight: 58.54 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43172 (Residues: 1-522; Coverage: 100%)
Gene names: PRP4, PRPF4
Sequence domains:
U4/U6 small nuclear ribonucleoprotein Prp31 Chain: 4D
Molecule details ›
Chain: 4D
Length: 499 amino acids
Theoretical weight: 55.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8WWY3 (Residues: 1-499; Coverage: 100%)
Gene names: PRP31, PRPF31
Sequence domains:
NHP2-like protein 1 Chain: 4E
Molecule details ›
Chain: 4E
Length: 128 amino acids
Theoretical weight: 14.19 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P55769 (Residues: 1-128; Coverage: 100%)
Gene names: NHP2L1, SNU13
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Thioredoxin-like protein 4A Chain: 4F
Molecule details ›
Chain: 4F
Length: 142 amino acids
Theoretical weight: 16.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P83876 (Residues: 1-142; Coverage: 100%)
Gene names: DIM1, TXNL4, TXNL4A
Sequence domains: Mitosis protein DIM1
Pre-mRNA-processing factor 6 Chain: 4G
Molecule details ›
Chain: 4G
Length: 941 amino acids
Theoretical weight: 107.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O94906 (Residues: 1-941; Coverage: 100%)
Gene names: C20orf14, PRPF6
Sequence domains:
RNA-binding protein 42 Chain: 4R
Molecule details ›
Chain: 4R
Length: 480 amino acids
Theoretical weight: 50.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BTD8 (Residues: 1-480; Coverage: 100%)
Gene name: RBM42
Sequence domains: RNA recognition motif
U4/U6.U5 tri-snRNP-associated protein 1 Chain: 4S
Molecule details ›
Chain: 4S
Length: 800 amino acids
Theoretical weight: 90.41 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43290 (Residues: 1-800; Coverage: 100%)
Gene name: SART1
Sequence domains:
Ubiquitin carboxyl-terminal hydrolase 39 Chain: 4T
Molecule details ›
Chain: 4T
Length: 565 amino acids
Theoretical weight: 65.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q53GS9 (Residues: 1-565; Coverage: 100%)
Gene names: CGI-21, HSPC332, PRO2855, USP39
Sequence domains:
Probable ATP-dependent RNA helicase DDX23 Chain: 4U
Molecule details ›
Chain: 4U
Length: 820 amino acids
Theoretical weight: 95.79 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BUQ8 (Residues: 1-820; Coverage: 100%)
Gene name: DDX23
Sequence domains:
U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein Chain: 4X
Molecule details ›
Chain: 4X
Length: 155 amino acids
Theoretical weight: 18.92 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8WVK2 (Residues: 1-155; Coverage: 100%)
Gene name: SNRNP27
Sequence domains: U4/U6.U5 small nuclear ribonucleoproteins
Serine/threonine-protein kinase PRP4 homolog Chain: 4Y
Molecule details ›
Chain: 4Y
Length: 1007 amino acids
Theoretical weight: 117.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13523 (Residues: 1-1007; Coverage: 100%)
Gene names: KIAA0536, PRP4, PRP4B, PRP4H, PRP4K, PRPF4K
Sequence domains: Protein kinase domain
U2 small nuclear ribonucleoprotein A' Chain: 2B
Molecule details ›
Chain: 2B
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: 2C
Molecule details ›
Chain: 2C
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
Splicing factor 3A subunit 1 Chain: 2D
Molecule details ›
Chain: 2D
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 2 Chain: 2E
Molecule details ›
Chain: 2E
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: 2F
Molecule details ›
Chain: 2F
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:
Splicing factor 3B subunit 1 Chain: 2G
Molecule details ›
Chain: 2G
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 2 Chain: 2H
Molecule details ›
Chain: 2H
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: 2I
Molecule details ›
Chain: 2I
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: 2J
Molecule details ›
Chain: 2J
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: 2K
Molecule details ›
Chain: 2K
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: 2L
Molecule details ›
Chain: 2L
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: 2M
Molecule details ›
Chain: 2M
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)
pre-mRNA Chain: A
Molecule details ›
Chain: A
Length: 144 nucleotides
Theoretical weight: 45.96 KDa
U6 snRNA Chain: 6A
Molecule details ›
Chain: 6A
Length: 107 nucleotides
Theoretical weight: 34.4 KDa
Sequence domains: U6 spliceosomal RNA
U5 snRNA Chain: 5A
Molecule details ›
Chain: 5A
Length: 117 nucleotides
Theoretical weight: 37.25 KDa
Sequence domains: U5 spliceosomal RNA
U4 snRNA Chain: 4A
Molecule details ›
Chain: 4A
Length: 146 nucleotides
Theoretical weight: 47 KDa
Sequence domains: U4 spliceosomal RNA
U2 snRNA Chain: 2A
Molecule details ›
Chain: 2A
Length: 188 nucleotides
Theoretical weight: 60.19 KDa
Sequence domains: U2 spliceosomal RNA

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-34500

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