9L12 | pdb_00009l12

Crystal structure of Cas12h ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.81 Å
  • R-Value Free: 
    0.339 (Depositor), 0.347 (DCC) 
  • R-Value Work: 
    0.334 (Depositor), 0.336 (DCC) 
  • R-Value Observed: 
    0.335 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


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Literature

Cas12h is a crRNA-guided DNA nickase that can be utilized for precise gene editing.

Xiang, W.Lin, X.Yang, Y.Huang, L.Chen, Y.Chen, J.Liu, L.

(2025) Cell Rep 44: 115718-115718

  • DOI: https://doi.org/10.1016/j.celrep.2025.115718
  • Primary Citation of Related Structures:  
    9L12

  • PubMed Abstract: 

    Type V-H CRISPR-Cas system, an important subtype of type V CRISPR-Cas systems, has remained enigmatic in terms of its structure and function despite being discovered several years ago. Here, we comprehensively characterize the type V-H CRISPR-Cas system and elucidate its role as a DNA nicking system. The unique CRISPR RNA (crRNA) employed by Cas12h effector protein enables specific targeting of double-stranded DNA (dsDNA), while its RuvC domain is responsible for cleaving the non-target strand (NTS) of dsDNA. We present the structure of Cas12h bound to crRNA and target DNA. Our structural analysis reveals that the RuvC domain possesses a narrow active pocket that facilitates recognition of NTS but potentially hinders access to the target strand. Furthermore, we demonstrate that Cas12h confers adaptive immunity against invading mobile genetic elements through transcriptional gene inhibition. We have engineered an adenine base editor by fusing Cas12h with an adenine deaminase, achieving effective A-to-G substitution.


  • Organizational Affiliation
    • State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cas12h
A, E, I
870unidentifiedMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (28-MER)
B, F, J
28synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*GP*TP*CP*GP*AP*TP*GP*TP*TP*CP*T)-3')
C, G, K
15synthetic construct
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (56-MER)
D, H, L
56unidentified
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.81 Å
  • R-Value Free:  0.339 (Depositor), 0.347 (DCC) 
  • R-Value Work:  0.334 (Depositor), 0.336 (DCC) 
  • R-Value Observed: 0.335 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.527α = 90
b = 155.527β = 90
c = 479.655γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release