6WMI

ZNF410 zinc fingers 1-5 with 17 mer blunt DNA Oligonucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

ZNF410 Uniquely Activates the NuRD Component CHD4 to Silence Fetal Hemoglobin Expression.

Lan, X.Ren, R.Feng, R.Ly, L.C.Lan, Y.Zhang, Z.Aboreden, N.Qin, K.Horton, J.R.Grevet, J.D.Mayuranathan, T.Abdulmalik, O.Keller, C.A.Giardine, B.Hardison, R.C.Crossley, M.Weiss, M.J.Cheng, X.Shi, J.Blobel, G.A.

(2021) Mol Cell 81: 239-254.e8

  • DOI: https://doi.org/10.1016/j.molcel.2020.11.006
  • Primary Citation of Related Structures:  
    6WMI

  • PubMed Abstract: 

    Metazoan transcription factors typically regulate large numbers of genes. Here we identify via a CRISPR-Cas9 genetic screen ZNF410, a pentadactyl DNA-binding protein that in human erythroid cells directly activates only a single gene, the NuRD component CHD4. Specificity is conveyed by two highly evolutionarily conserved clusters of ZNF410 binding sites near the CHD4 gene with no counterparts elsewhere in the genome. Loss of ZNF410 in adult-type human erythroid cell culture systems and xenotransplantation settings diminishes CHD4 levels and derepresses the fetal hemoglobin genes. While previously known to be silenced by CHD4, the fetal globin genes are exposed here as among the most sensitive to reduced CHD4 levels.. In vitro DNA binding assays and crystallographic studies reveal the ZNF410-DNA binding mode. ZNF410 is a remarkably selective transcriptional activator in erythroid cells, and its perturbation might offer new opportunities for treatment of hemoglobinopathies.


  • Organizational Affiliation

    Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein 410A,
B [auth D]
155Homo sapiensMutation(s): 0 
Gene Names: ZNF410APA1
UniProt & NIH Common Fund Data Resources
Find proteins for Q86VK4 (Homo sapiens)
Explore Q86VK4 
Go to UniProtKB:  Q86VK4
GTEx:  ENSG00000119725 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86VK4
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*AP*CP*AP*TP*CP*CP*CP*AP*TP*AP*AP*TP*AP*AP*TP*G)-3')C [auth B],
E
17Homo sapiens
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*AP*TP*TP*AP*TP*TP*AP*TP*GP*GP*GP*AP*TP*GP*TP*G)-3')D [auth C],
F
17Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth D],
N [auth D],
O [auth D],
P [auth D],
Q [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
R [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.257α = 90
b = 186.257β = 90
c = 46.95γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references