2NN2 | pdb_00002nn2

Crystal structure of the BTB domain from the LRF/ZBTB7 transcriptional regulator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.267 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the BTB domain from the LRF/ZBTB7 transcriptional regulator.

Stogios, P.J.Chen, L.Prive, G.G.

(2007) Protein Sci 16: 336-342

  • DOI: https://doi.org/10.1110/ps.062660907
  • Primary Citation Related Structures: 
    2NN2

  • PubMed Abstract: 

    BTB-zinc finger (BTB-ZF) proteins are transcription regulators with roles in development, differentiation, and oncogenesis. In these proteins, the BTB domain (also known as the POZ domain) is a protein-protein interaction motif that contains a dimerization interface, a possible oligomerization surface, and surfaces for interactions with other factors, including nuclear co-repressors and histone deacetylases. The BTB-ZF protein LRF (also known as ZBTB7, FBI-1, OCZF, and Pokemon) is a master regulator of oncogenesis, and represses the transcription of a variety of important genes, including the ARF, c-fos, and c-myc oncogenes and extracellular matrix genes. We determined the crystal structure of the BTB domain from human LRF to 2.1 A and observed the canonical BTB homodimer fold. However, novel features are apparent on the surface of the homodimer, including differences in the lateral groove and charged pocket regions. The residues that line the lateral groove have little similarity with the equivalent residues from the BCL6 BTB domain, and we show that the 17-residue BCL6 Binding Domain (BBD) from the SMRT co-repressor does not bind to the LRF BTB domain.


  • Organizational Affiliation
    • Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario, Canada.

Macromolecule Content 

  • Total Structure Weight: 28.33 kDa 
  • Atom Count: 1,882 
  • Modeled Residue Count: 234 
  • Deposited Residue Count: 266 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc finger and BTB domain-containing protein 7A
A, B
133Homo sapiensMutation(s): 0 
Gene Names: ZBTB7AFBI1LRFZBTB7
UniProt & NIH Common Fund Data Resources
Find proteins for O95365 (Homo sapiens)
Explore O95365 
Go to UniProtKB:  O95365
PHAROS:  O95365
GTEx:  ENSG00000178951 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95365
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.267 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.143α = 90
b = 72.143β = 90
c = 116.048γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description