› 7evo

Electron Microscopy
2.5Å resolution

The cryo-EM structure of the human 17S U2 snRNP

Released:
DOI: 10.2210/pdb7evo/pdb
PDB entry 7evo coloured by chain, front view.
PDB entry 7evo coloured by chain, side view.
PDB entry 7evo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into branch site proofreading by human spliceosome
Zhang X, Zhan X, Bian T, Yang F, Li P, Lu Y, Xing Z, Fan R, Zhang QC, Shi Y
Nat. Struct. Mol. Biol. (2024)
Related structures: EMD-31334

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 21-mer (preferred)
PDBe Complex ID:
PDB-CPX-129082 (preferred)
Entry contents:
20 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (21 distinct):
Splicing factor 3B subunit 1 Chain: 1
Molecule details ›
Chain: 1
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: 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: 135.72 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: 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 5 Chain: 5
Molecule details ›
Chain: 5
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: 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 3A subunit 1 Chain: A
Molecule details ›
Chain: A
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: B
Molecule details ›
Chain: B
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: C
Molecule details ›
Chain: C
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:
17S U2 SnRNP complex component HTATSF1 Chain: D
Molecule details ›
Chain: D
Length: 755 amino acids
Theoretical weight: 85.97 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43719 (Residues: 1-755; Coverage: 100%)
Gene name: HTATSF1
Sequence domains: RNA recognition motif
Probable ATP-dependent RNA helicase DDX46 Chain: E
Molecule details ›
Chain: E
Length: 1052 amino acids
Theoretical weight: 119.81 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q7L014 (Residues: 1-870, 871-1031; Coverage: 100%)
Gene names: DDX46, KIAA0801
Sequence domains:
U2 small nuclear ribonucleoprotein A' Chain: F
Molecule details ›
Chain: F
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: G
Molecule details ›
Chain: G
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
Small nuclear ribonucleoprotein Sm D2 Chain: a
Molecule details ›
Chain: a
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 Chain: b
Molecule details ›
Chain: b
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: c
Molecule details ›
Chain: c
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 Chain: d
Molecule details ›
Chain: d
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 Chain: e
Molecule details ›
Chain: e
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' Chain: f
Molecule details ›
Chain: f
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 Chain: g
Molecule details ›
Chain: g
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
U2 snRNA Chain: H
Molecule details ›
Chain: H
Length: 188 nucleotides
Theoretical weight: 60.19 KDa
Sequence domains: U2 spliceosomal RNA

Ligands and Environments

2 bound ligands:
Ligand 9B0 1 x 9B0
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.5Å
Relevant EMDB volumes: EMD-31334
Expression system: Homo sapiens

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