7N5S

ZBTB7A Zinc Finger Domain Bound to -200 Site of Fetal Globin Promoter (Oligo 6)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural basis for human ZBTB7A action at the fetal globin promoter.

Yang, Y., Ren, R., Ly, L.C., Horton, J.R., Li, F., Quinlan, K.G.R., Crossley, M., Shi, Y., Cheng, X.

(2021) Cell Rep 36: 109759-109759

  • DOI: 10.1016/j.celrep.2021.109759
  • Primary Citation of Related Structures:  
    7EYI, 7N5S, 7N5T

  • PubMed Abstract: 

    • Elevated levels of fetal globin protect against β-hemoglobinopathies, such as sickle cell disease and β-thalassemia. Two zinc-finger (ZF) repressors, BCL11A and ZBTB7A/LRF, bind directly to the fetal globin promoter elements positioned at -115 and -200, respectively ...

    Elevated levels of fetal globin protect against β-hemoglobinopathies, such as sickle cell disease and β-thalassemia. Two zinc-finger (ZF) repressors, BCL11A and ZBTB7A/LRF, bind directly to the fetal globin promoter elements positioned at -115 and -200, respectively. Here, we describe X-ray structures of the ZBTB7A DNA-binding domain, consisting of four adjacent ZFs, in complex with the -200 sequence element, which contains two copies of four consecutive C:G base pairs. ZF1 and ZF2 recognize the 5' C:G quadruple, and ZF4 contacts the 3' C:G quadruple. Natural non-coding DNA mutations associated with hereditary persistence of fetal hemoglobin (HPFH) impair ZBTB7A DNA binding, with the most severe disruptions resulting from mutations in the base pairs recognized by ZF1 and ZF2. Our results firmly establish ZBTB7A/LRF as a key molecular regulator of fetal globin expression and inform genome-editing strategies that inhibit repressor binding and boost fetal globin expression to treat hemoglobinopathies.

    Organizational Affiliation: 

    Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: xcheng5@mdanderson.org.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger and BTB domain-containing protein 7AA143Homo sapiensMutation(s): 0 
Gene Names: ZBTB7A, FBI1, LRF, ZBTB7, ZNF857A
UniProt & NIH Common Fund Data Resources
Find proteins for O95365 (Homo sapiens)
Explore O95365 
Go to UniProtKB:  O95365
PHAROS:  O95365
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95365
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA Strand IB [auth X]15Homo sapiens
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA Strand IIC [auth Y]15Homo sapiens
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.938α = 90
b = 36.963β = 100.012
c = 74.257γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM049245-23

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Database references