6WMI | pdb_00006wmi

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

• PDB DOI: https://doi.org/10.2210/pdb6WMI/pdb
• NAKB: 6WMI

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-04-21 Released: 2020-12-09 
• Deposition Author(s): Ren, R., Horton, J.R., Cheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

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

• PubMed: 33301730 
• DOI: https://doi.org/10.1016/j.molcel.2020.11.006
• Primary Citation 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.

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Organizational Affiliation: 
• Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, NSW 2052, Australia.
Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: [e-mail].
Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.91 kDa 
• Atom Count: 3,803 
• Modeled Residue Count: 360 
• Deposited Residue Count: 378 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger protein 410	A, B [auth D]	155	Homo sapiens	Mutation(s): 0  Gene Names: ZNF410, APA1
UniProt & NIH Common Fund Data Resources
Find proteins for Q86VK4 (Homo sapiens) Explore Q86VK4  Go to UniProtKB:  Q86VK4
GTEx:  ENSG00000119725

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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	17	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
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	17	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	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	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 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 186.257	α = 90
b = 186.257	β = 90
c = 46.95	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Ren, R., Horton, J.R., Cheng, X.

Revision History  

• 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