› 6v4x

Electron Microscopy
3.2Å resolution

Cryo-EM structure of an active human histone pre-mRNA 3'-end processing machinery at 3.2 Angstrom resolution

Released:
DOI: 10.2210/pdb6v4x/pdb
PDB entry 6v4x coloured by chain, front view.
PDB entry 6v4x coloured by chain, side view.
PDB entry 6v4x coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of an active human histone pre-mRNA 3'-end processing machinery.
Sun Y, Zhang Y, Aik WS, Yang XC, Marzluff WF, Walz T, Dominski Z, Tong L
Science 367 700-703 (2020)
PMID: 32029631
Related structures: EMD-21050

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147024 (preferred)
Entry contents:
10 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (12 distinct):
Small nuclear ribonucleoprotein Sm D3 Chain: A
Molecule details ›
Chain: A
Length: 146 amino acids
Theoretical weight: 16.11 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62318 (Residues: 1-126; Coverage: 100%)
Gene name: SNRPD3
Sequence domains: LSM domain
Small nuclear ribonucleoprotein-associated proteins B and B' Chain: B
Molecule details ›
Chain: B
Length: 95 amino acids
Theoretical weight: 10.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P14678 (Residues: 1-95; Coverage: 40%)
Gene names: COD, SNRPB, SNRPB1
Sequence domains: LSM domain
Small nuclear ribonucleoprotein F Chain: F
Molecule details ›
Chain: F
Length: 86 amino acids
Theoretical weight: 9.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62306 (Residues: 1-86; Coverage: 100%)
Gene names: PBSCF, SNRPF
Sequence domains: LSM domain
Small nuclear ribonucleoprotein E Chain: E
Molecule details ›
Chain: E
Length: 92 amino acids
Theoretical weight: 10.82 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62304 (Residues: 1-92; Coverage: 100%)
Gene name: SNRPE
Sequence domains: LSM domain
Small nuclear ribonucleoprotein G Chain: G
Molecule details ›
Chain: G
Length: 84 amino acids
Theoretical weight: 9.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62308 (Residues: 1-76; Coverage: 100%)
Gene names: PBSCG, SNRPG
Sequence domains: LSM domain
U7 snRNA-associated Sm-like protein LSm10 Chain: C
Molecule details ›
Chain: C
Length: 123 amino acids
Theoretical weight: 14.1 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q969L4 (Residues: 1-123; Coverage: 100%)
Gene name: LSM10
Sequence domains: LSM domain
U7 snRNA-associated Sm-like protein LSm11 Chain: D
Molecule details ›
Chain: D
Length: 259 amino acids
Theoretical weight: 28.61 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P83369 (Residues: 1-360; Coverage: 69%)
Gene name: LSM11
Cleavage and polyadenylation specificity factor subunit 3 Chain: H
Molecule details ›
Chain: H
Length: 684 amino acids
Theoretical weight: 77.58 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9UKF6 (Residues: 1-684; Coverage: 100%)
Gene names: CPSF3, CPSF73
Sequence domains:
Cleavage and polyadenylation specificity factor subunit 2 Chain: I
Molecule details ›
Chain: I
Length: 782 amino acids
Theoretical weight: 88.6 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9P2I0 (Residues: 1-782; Coverage: 100%)
Gene names: CPSF100, CPSF2, KIAA1367
Sequence domains:
Symplekin Chain: J
Molecule details ›
Chain: J
Length: 1072 amino acids
Theoretical weight: 120.36 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q92797 (Residues: 30-1101; Coverage: 84%)
Gene names: SPK, SYMPK
Sequence domains:
U7 snRNA Chain: Z
Molecule details ›
Chain: Z
Length: 60 nucleotides
Theoretical weight: 19.1 KDa
Sequence domains: U7 small nuclear RNA
modified H2a pre-mRNA Chain: Y
Molecule details ›
Chain: Y
Length: 52 nucleotides
Theoretical weight: 16.63 KDa
Sequence domains: Histone 3' UTR stem-loop

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-21050
Expression systems:
  • Escherichia coli BL21(DE3)
  • Trichoplusia ni

Quick links

Citations

13 review citations

Recent molecular insights into canonical pre-mRNA 3'-end processing.
Sun et al. (2020)
12 more

7 mentions without citation

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches.
Gerovac et al. (2021)
6 more