› 1xmm

X-ray diffraction
2.5Å resolution

Structure of human Dcps bound to m7GDP

Released:
DOI: 10.2210/pdb1xmm/pdb
PDB entry 1xmm coloured by chain, front view.
PDB entry 1xmm coloured by chain, side view.
PDB entry 1xmm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping.
Chen N, Walsh MA, Liu Y, Parker R, Song H
J Mol Biol 347 707-18 (2005)
PMID: 15769464

Function and Biology Details

Reaction catalysed: 
A 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] + H(2)O = N(7)-methylguanosine 5'-phosphate + a 5'-diphospho-[mRNA]
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188399 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
m7GpppX diphosphatase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 342 amino acids
Theoretical weight: 39.07 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96C86 (Residues: 1-337; Coverage: 100%)
Gene names: DCPS, DCS1, HINT5, HSPC015
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand PO4 4 x PO4
Ligand G7M 2 x G7M
Ligand M7G 2 x M7G
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL40B2
Spacegroup: P212121
Unit cell:
a: 100.928Å b: 105.14Å c: 138.647Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.214 0.267
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Early nonsense: mRNA decay solves a translational problem.
Amrani et al. (2006)
4 more

5 mentions without citation

La-related protein 1 (LARP1) binds the mRNA cap, blocking eIF4F assembly on TOP mRNAs.
Lahr et al. (2017)
4 more