3U21

Crystal structure of a Fragment of Nuclear factor related to kappa-B-binding protein (residues 370-495) (NFRKB) from Homo sapiens at 2.18 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a Novel Winged-Helix Like Domain from Human NFRKB Protein.

Kumar, A.Mocklinghoff, S.Yumoto, F.Jaroszewski, L.Farr, C.L.Grzechnik, A.Nguyen, P.Weichenberger, C.X.Chiu, H.J.Klock, H.E.Elsliger, M.A.Deacon, A.M.Godzik, A.Lesley, S.A.Conklin, B.R.Fletterick, R.J.Wilson, I.A.

(2012) Plos One 7: e43761-e43761

  • DOI: 10.1371/journal.pone.0043761

  • PubMed Abstract: 
  • The human nuclear factor related to kappa-B-binding protein (NFRKB) is a 1299-residue protein that is a component of the metazoan INO80 complex involved in chromatin remodeling, transcription regulation, DNA replication and DNA repair. Although full ...

    The human nuclear factor related to kappa-B-binding protein (NFRKB) is a 1299-residue protein that is a component of the metazoan INO80 complex involved in chromatin remodeling, transcription regulation, DNA replication and DNA repair. Although full length NFRKB is predicted to be around 65% disordered, comparative sequence analysis identified several potentially structured sections in the N-terminal region of the protein. These regions were targeted for crystallographic studies, and the structure of one of these regions spanning residues 370-495 was determined using the JCSG high-throughput structure determination pipeline. The structure reveals a novel, mostly helical domain reminiscent of the winged-helix fold typically involved in DNA binding. However, further analysis shows that this domain does not bind DNA, suggesting it may belong to a small group of winged-helix domains involved in protein-protein interactions.


    Organizational Affiliation

    Joint Center for Structural Genomics, La Jolla, California, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear factor related to kappa-B-binding protein
A, B
127Homo sapiensMutation(s): 0 
Gene Names: NFRKB (INO80G)
Find proteins for Q6P4R8 (Homo sapiens)
Go to Gene View: NFRKB
Go to UniProtKB:  Q6P4R8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
MLY
Query on MLY
A, B
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 60.942α = 90.00
b = 60.942β = 90.00
c = 130.839γ = 90.00
Software Package:
Software NamePurpose
SHELXDphasing
XDSdata reduction
SHELXphasing
XSCALEdata scaling
MolProbitymodel building
REFMACrefinement
PDB_EXTRACTdata extraction
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2012-10-10
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description