2FV2

Crystal Structure Analysis of human Rcd-1 conserved region


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Atomic model of human Rcd-1 reveals an armadillo-like-repeat protein with in vitro nucleic acid binding properties.

Garces, R.G.Gillon, W.Pai, E.F.

(2007) Protein Sci. 16: 176-188

  • DOI: 10.1110/ps.062600507

  • PubMed Abstract: 
  • Rcd-1, a protein highly conserved across eukaryotes, was initially identified as a factor essential for nitrogen starvation-invoked differentiation in fission yeast, and its Saccharomyces cerevisiae homolog, CAF40, has been identified as part of the ...

    Rcd-1, a protein highly conserved across eukaryotes, was initially identified as a factor essential for nitrogen starvation-invoked differentiation in fission yeast, and its Saccharomyces cerevisiae homolog, CAF40, has been identified as part of the CCR4-NOT transcription complex, where it interacts with the NOT1 protein. Mammalian homologs are involved in various cellular differentiation processes including retinoic acid-induced differentiation and hematopoetic cell development. Here, we present the 2.2 A X-ray structure of the highly conserved region of human Rcd-1 and investigate possible functional abilities of this and the full-length protein. The monomer is made up of six armadillo repeats forming a solvent-accessible, positively-charged cleft 21-22 A wide that, in contrast to other armadillo proteins, stays fully exposed in the dimer. Prompted by this finding, we established that Rcd-1 can bind to single- and double-stranded oligonucleotides in vitro with the affinity of G/C/T > A. Mutation of an arginine residue within the cleft strongly reduced or abolished oligonucleotide binding. Rcd-1's ability to bind to nucleic acids, in addition to the previously reported protein-protein interaction with NOT1, suggests a new feature in Rcd-1's role in regulation of overall cellular differentiation processes.


    Organizational Affiliation

    Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RCD1 required for cell differentiation1 homolog
A, B, C, D
268Homo sapiensGene Names: RQCD1 (CNOT9, RCD1)
Find proteins for Q92600 (Homo sapiens)
Go to UniProtKB:  Q92600
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.217 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 68.508α = 94.16
b = 68.963β = 117.26
c = 69.361γ = 91.91
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
SnBphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-01-09
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description