› 6l5m

X-ray diffraction
2.7Å resolution

Crystal structure of human DEAD-box RNA helicase DDX21 in complex with AMP

Released:
DOI: 10.2210/pdb6l5m/pdb
PDB entry 6l5m coloured by chain, front view.
PDB entry 6l5m coloured by chain, side view.
PDB entry 6l5m coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation.
Chen Z, Li Z, Hu X, Xie F, Kuang S, Zhan B, Gao W, Chen X, Gao S, Li Y, Wang Y, Qian F, Ding C, Gan J, Ji C, Xu XW, Zhou Z, Huang J, He HH, Li J
Adv Sci (Weinh) 7 2000532 (2020)
PMID: 32714761

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192533 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleolar RNA helicase 2 Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 377 amino acids
Theoretical weight: 42.28 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NR30 (Residues: 188-563; Coverage: 48%)
Gene name: DDX21
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand AMP 5 x AMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P21
Unit cell:
a: 36.39Å b: 219.07Å c: 126.39Å
α: 90° β: 90.79° γ: 90°
R-values:
R R work R free
0.21 0.207 0.257
Expression system: Escherichia coli

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Citations

2 review citations

Long noncoding RNA and protein abundance in lncRNPs.
Wu et al. (2021)
1 more

2 mentions without citation

Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation.
Chen et al. (2020)
1 more