Crystal structure of ZAD-domain of Serendipity-d protein from D.melanogaster

Experimental Data Snapshot

  • Resolution: 2.85 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structural insights into highly similar spatial organization of zinc-finger associated domains with a very low sequence similarity.

Bonchuk, A.N.Boyko, K.M.Nikolaeva, A.Y.Burtseva, A.D.Popov, V.O.Georgiev, P.G.

(2022) Structure 30: 1004

  • DOI: https://doi.org/10.1016/j.str.2022.04.009
  • Primary Citation of Related Structures:  
    7PO9, 7POH, 7POK, 7PPP

  • PubMed Abstract: 

    ZAD is a C4 zinc-coordinating domain often found at the N-terminus mostly of arthropodan transcription factors with multiple C2H2 zinc-finger domains involved in the regulation of chromosome architecture and promotor activity. ZADs predominantly form homodimers and have low primary sequence similarity. We obtained three crystal structures of the most phylogenetically distant Drosophila ZADs and structure of the only known ZAD-like domain from a mammalian protein (ZNF276). All ZAD structures demonstrate unity of the spatial fold as well as some unique structural features. The specific homodimerization of ZAD is primarily determined by the position and size of secondary structural elements and is further strengthened by a number of unique interactions between subunits. Structural comparison allowed for unraveling key sequence features underlying the similarity of the spatial fold. These features result in a broad variety of ZADs in Arthropod C2H2 proteins, allowing for the emergence of a wide range of highly specific homodimers.

  • Organizational Affiliation

    Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia. Electronic address: bonchuk_a@genebiology.ru.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serendipity locus protein delta
A, B
96Drosophila melanogasterMutation(s): 0 
Gene Names: Sry-deltaSry-dCG17958
Find proteins for P07664 (Drosophila melanogaster)
Explore P07664 
Go to UniProtKB:  P07664
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07664
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.85 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.161α = 90
b = 99.161β = 90
c = 117.667γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation19-74-10099

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references
  • Version 1.2: 2022-07-20
    Changes: Database references