2IF5 | pdb_00002if5

Structure of the POZ domain of human LRF, a master regulator of oncogenesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.291 (Depositor), 0.293 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Structure of the POZ domain of human LRF, a master regulator of oncogenesis.

Schubot, F.D.Tropea, J.E.Waugh, D.S.

(2006) Biochem Biophys Res Commun 351: 1-6

  • DOI: https://doi.org/10.1016/j.bbrc.2006.09.167
  • Primary Citation Related Structures: 
    2IF5

  • PubMed Abstract: 

    The proto-oncogenic properties of the POK family of transcriptional repressors BCL6, PLZF, and LRF have been well established. These proteins utilize their amino-terminal POZ domains for multimerization and the recruitment of co-repressors. Because LRF represses the production of the tumor suppressor p19(Arf) (ARF), it is regarded as an attractive therapeutic target for the treatment of many types of cancer. The crystal structure of the LRF POZ domain reveals a high degree of structural conservation with the corresponding domains of BCL6 and PLZF. However, striking differences between the electrostatic properties of the BCL6 and LRF POZ domains suggest that if, like BCL6, LRF interacts with the co-repressor SMRT, it almost certainly uses a different mechanism to do so. These differences may also explain why LRF interacts with BCL6 but not with PLZF. Finally, the conservation of crystal packing contacts suggests the probable location of the interface that mediates LRF/BCL6 complex formation.


  • Organizational Affiliation
    • Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702-1201, USA.

Macromolecule Content 

  • Total Structure Weight: 13.36 kDa 
  • Atom Count: 997 
  • Modeled Residue Count: 115 
  • Deposited Residue Count: 120 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc finger and BTB domain-containing protein 7A120Homo 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: 2.00 Å
  • R-Value Free:  0.291 (Depositor), 0.293 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.85α = 90
b = 65.85β = 90
c = 162.603γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data 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: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description