8TLO | pdb_00008tlo

Crystal Structure Analysis of BCL11A in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 
    0.269 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.252 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.253 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into the DNA-binding mechanism of BCL11A: The integral role of ZnF6.

Viennet, T.Yin, M.Jayaraj, A.Kim, W.Sun, Z.J.Fujiwara, Y.Zhang, K.Seruggia, D.Seo, H.S.Dhe-Paganon, S.Orkin, S.H.Arthanari, H.

(2024) Structure 32: 2276-2286.e4

  • DOI: https://doi.org/10.1016/j.str.2024.09.022
  • Primary Citation of Related Structures:  
    8THO, 8TLO

  • PubMed Abstract: 

    The transcription factor BCL11A is a critical regulator of the switch from fetal hemoglobin (HbF: α 2 γ 2 ) to adult hemoglobin (HbA: α 2 β 2 ) during development. BCL11A binds at a cognate recognition site (TGACCA) in the γ-globin gene promoter and represses its expression. DNA-binding is mediated by a triple zinc finger domain, designated ZnF456. Here, we report comprehensive investigation of ZnF456, leveraging X-ray crystallography and NMR to determine the structures in both the presence and absence of DNA. We delve into the dynamics and mode of interaction with DNA. Moreover, we discovered that the last zinc finger of BCL11A (ZnF6) plays a different role compared to ZnF4 and 5, providing a positive entropic contribution to DNA binding and γ-globin gene repression. Comprehending the DNA binding mechanism of BCL11A opens avenues for the strategic, structure-based design of novel therapeutics targeting sickle cell disease and β-thalassemia.


  • Organizational Affiliation

    Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B-cell lymphoma/leukemia 11A110Homo sapiensMutation(s): 0 
Gene Names: BCL11ACTIP1EVI9KIAA1809ZNF856
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H165 (Homo sapiens)
Explore Q9H165 
Go to UniProtKB:  Q9H165
PHAROS:  Q9H165
GTEx:  ENSG00000119866 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H165
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free:  0.269 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.252 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.253 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.74α = 90
b = 60.87β = 108.2
c = 78.35γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
XDSdata reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Database references, Structure summary
  • Version 1.2: 2024-11-06
    Changes: Database references
  • Version 1.3: 2024-12-18
    Changes: Database references