9J89 | pdb_00009j89

zbp1 nucleic acid complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.245 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

ZBP1 senses spliceosome stress through Z-RNA:DNA hybrid recognition.

He, J.Zhu, Y.Tian, Z.Liu, M.Gao, A.Fu, W.Lu, F.Sun, Y.Guo, Y.Pan, R.Ji, Y.Chen, J.Lu, H.Lin, J.Liang, X.Kim, C.Zhou, C.Jiao, H.

(2025) Mol Cell 85: 1790-1805.e7

  • DOI: https://doi.org/10.1016/j.molcel.2025.04.004
  • Primary Citation of Related Structures:  
    9J89, 9J8G

  • PubMed Abstract: 

    Z-DNA-binding protein 1 (ZBP1; also known as DAI or DLM-1) regulates cell death and inflammation by sensing left-handed double-helical nucleic acids, including Z-RNA and Z-DNA. However, the physiological conditions that generate Z-form nucleic acids (Z-NAs) and activate ZBP1-dependent signaling pathways remain largely elusive. In this study, we developed a probe, Zα-mFc, that specifically detected both Z-DNA and Z-RNA. Utilizing this probe, we discovered that inhibiting spliceosome causes nuclear accumulation of Z-RNA:DNA hybrids, which are sensed by ZBP1 via its Zα domains, triggering apoptosis and necroptosis in mammalian cells. Furthermore, we solved crystal structures of the human or mouse Zα1 domain complexed with a 6-bp RNA:DNA hybrid, revealing that the RNA:DNA hybrid adopts a left-handed conformation. Our findings demonstrate that the spliceosome acts as a checkpoint preventing accumulation of Z-RNA:DNA hybrids, which potentially function as endogenous ligands activating ZBP1-dependent cell death pathways.


  • Organizational Affiliation
    • Zhejiang Key Laboratory of Molecular Cancer Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; Department of Neonatal Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China.

Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Z-DNA-binding protein 1C [auth D],
D [auth F],
E [auth H],
F [auth A]
64Homo sapiensMutation(s): 0 
Gene Names: ZBP1C20orf183DLM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H171 (Homo sapiens)
Explore Q9H171 
Go to UniProtKB:  Q9H171
PHAROS:  Q9H171
GTEx:  ENSG00000124256 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H171
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*AP*CP*GP*CP*A)-3')A [auth C],
B [auth G]
6Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R(P*UP*GP*CP*GP*UP*G)-3')G [auth E],
H [auth B]
6Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth C]
J [auth C]
K [auth G]
L [auth G]
M [auth D]
I [auth C],
J [auth C],
K [auth G],
L [auth G],
M [auth D],
N [auth F],
O [auth A],
P [auth E],
Q [auth E],
R [auth B],
S [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.245 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.24α = 90
b = 173.95β = 94.42
c = 30.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release