8I6K

Structure of hMNDA HIN with dsDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

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Literature

Structural mechanism of dsDNA recognition by the hMNDA HIN domain: New insights into the DNA-binding model of a PYHIN protein.

Li, Y.Zhang, C.Samad, A.Zheng, P.Li, Y.Chen, F.Jin, T.

(2023) Int J Biol Macromol 245: 125461-125461

  • DOI: https://doi.org/10.1016/j.ijbiomac.2023.125461
  • Primary Citation of Related Structures:  
    8I6K

  • PubMed Abstract: 

    The hematopoietic interferon-inducible nuclear (HIN) domain of the PYHIN family of proteins recognizes double-stranded DNA (dsDNA) through different dsDNA-binding modes. These modes apparently confer different roles upon these proteins in the regulation of innate immune responses, gene transcription, and apoptosis. Myeloid cell nuclear differentiation antigen (MNDA), a member of the human PYHIN family, binds DNA and regulates gene transcription in monocytes. However, the mechanism of DNA recognition and DNA-binding modes of human MNDA (hMNDA) remain unclear. Here, we determined the crystal structure of the hMNDA-HIN domain in complex with dsDNA at 2.4 Å resolution, and reveal that hMNDA-HIN binds to dsDNA in a sequence-independent manner. Structure and mutation studies indicated that hMNDA-HIN binds to dsDNA through a unique mode, involving two dsDNA-binding interfaces. Interface I exhibits an AIM2-like dsDNA-binding mode, and interface II has a previously unreported mode of dsDNA-binding. These results provide new insights into the DNA-binding modes of this PYHIN protein.


  • Organizational Affiliation

    Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myeloid cell nuclear differentiation antigen217Homo sapiensMutation(s): 0 
Gene Names: MNDA
UniProt & NIH Common Fund Data Resources
Find proteins for P41218 (Homo sapiens)
Explore P41218 
Go to UniProtKB:  P41218
PHAROS:  P41218
GTEx:  ENSG00000163563 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41218
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
B, C
12synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.652α = 90
b = 40.652β = 90
c = 138.76γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDPB29030104

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release