PDBsum entry: 2yt4

RNA binding protein

PDB id: 2yt4

Contents

Protein chain

196 a.a. *

Waters ×39

* Residue conservation analysis

PDB id:

2yt4

Name:

RNA binding protein

Title:

Crystal structure of human dgcr8 core

Structure:

Protein dgcr8. Chain: a. Fragment: two dsrbds and c-terminal domain. Synonym: digeorge syndrome critical region 8, digeorge syndrome chromosomal region. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Strain: hek293t. Gene: dgcr8, c22orf12, dgcrk6. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.60Å R-factor: 0.214 R-free: 0.269

Authors:

Y.Cho,S.Y.Sohn

Key ref:

S.Y.Sohn et al. (2007). Crystal structure of human DGCR8 core. Nat Struct Biol, 14, 847-853. PubMed id: 17704815 DOI: 10.1038/nsmb1294

Date:

05-Apr-07 Release date: 21-Aug-07

Protein chain

Q8WYQ5  (DGCR8_HUMAN) -  Microprocessor complex subunit DGCR8

Seq: 773 a.a.

Struc: 196 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (1 term)
• Biochemical function: RNA binding (2 terms)

DOI no: 10.1038/nsmb1294

Nat Struct Biol 14:847-853 (2007)

PubMed id: 17704815

Crystal structure of human DGCR8 core.

S.Y.Sohn, W.J.Bae, J.J.Kim, K.H.Yeom, V.N.Kim, Y.Cho.

ABSTRACT

A complex of Drosha with DGCR8 (or its homolog Pasha) cleaves primary microRNA (pri-miRNA) substrates into precursor miRNA and initiates the microRNA maturation process. Drosha provides the catalytic site for this cleavage, whereas DGCR8 or Pasha provides a frame for anchoring substrate pri-miRNAs. To clarify the molecular basis underlying recognition of pri-miRNA by DGCR8 and Pasha, we determined the crystal structure of the human DGCR8 core (DGCR8S, residues 493-720). In the structure, the two double-stranded RNA-binding domains (dsRBDs) are arranged with pseudo two-fold symmetry and are tightly packed against the C-terminal helix. The H2 helix in each dsRBD is important for recognition of pri-miRNA substrates. This structure, together with fluorescent resonance energy transfer and mutational analyses, suggests that the DGCR8 core recognizes pri-miRNA in two possible orientations. We propose a model for DGCR8's recognition of pri-miRNA.

Selected figure(s)

Figure 1.
(a) Schematic representation of DGCR8, containing the WW domain and two dsRBD domains. Also indicated are sequences spanned by two constructs of DGCR8 containing both dsRBDs. (b) Structural alignment of the two dsRBDs of human DGCR8. Conserved nucleotide-binding residues in three regions are highlighted yellow, pink and blue, respectively. Basic residues in dsRBD1 are highlighted green. Conserved sequence of dsRBDs is shown below in magenta. (c) DGCR8S structure. (d) dsRBD1 (blue) and dsRBD2 (red) have a pseudo two-fold symmetry axis. (e) Superposition of the structures of dsRBD1 and dsRBD2 of DGCR8. (f) Interactions between dsRBD1 and dsRBD2 and the C-terminal region. Key residues discussed in the text are shown in yellow. Dashed lines represent hydrogen bonds. Sulfur atoms are shown in orange.

Figure 3.
(a) The Xlrbpa–dsRNA complex structure^32 was superimposed on each dsRBD of DGCR8S, and its dsRNA structure was used as a model for RNA in the DGCR8–dsRNA complex. (b) Schematic illustrations of pri-miR-16-1 and the RNA-FAM-TMR dual-labeled pri-miRNA derivative (with positions of FAM and TMR fluorophores shown). Black arrows, Drosha cleavage sites; bold capital letters, pre-miRNA generated by Drosha–DGCR8; red, mature miRNA, which is assembled into the miRNA-induced silencing complex. (c,d) Normalized fluorescence spectra of RNA-FAM (RNA labeled with donor only; denoted by asterisk in key) and RNA-FAM-TMR (donor-acceptor dual-labeled RNA) in the presence or absence of DGCR8M. Keys indicate concentrations. (e) Schematic illustration of locations of FRET pair, tryptophan and AEDANS (Val581 position) in the DGCR8M structure. Residues Val581 and Trp665 are shown in cyan. (f) Normalized fluorescence spectra of DGCR8M-WC and DGCR8M-W-Ad in the presence or absence of pri-miR-16-1 at an excitation wavelength of 290 nm.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2007, 14, 847-853) copyright 2007.

Figures were selected by an automated process.