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 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1371/journal.pone.0043761
  • Primary Citation of Related Structures:  
    3U21

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear factor related to kappa-B-binding protein
A, B
127Homo sapiensMutation(s): 0 
Gene Names: BC063280INO80GNFRKB
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P4R8 (Homo sapiens)
Explore Q6P4R8 
Go to UniProtKB:  Q6P4R8
PHAROS:  Q6P4R8
GTEx:  ENSG00000170322 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P4R8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A, B
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.942α = 90
b = 60.942β = 90
c = 130.839γ = 90
Software Package:
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2012-10-10
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-02-01
    Changes: Database references, Derived calculations