Crystal structure of ZC3H12C PIN-CCCH Zn Finger domain with RNA heptamer

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

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PIN and CCCH Zn-finger domains coordinate RNA targeting in ZC3H12 family endoribonucleases.

Garg, A.Roske, Y.Yamada, S.Uehata, T.Takeuchi, O.Heinemann, U.

(2021) Nucleic Acids Res 49: 5369-5381

  • DOI: https://doi.org/10.1093/nar/gkab316
  • Primary Citation of Related Structures:  
    7NDH, 7NDI, 7NDJ, 7NDK

  • PubMed Abstract: 

    The CCCH-type zinc finger (ZnF) containing ZC3H12 ribonucleases are crucial in post-transcriptional immune homoeostasis with ZC3H12A being the only structurally studied member of the family. In this study, we present a structural-biochemical characterization of ZC3H12C, which is linked with chronic immune disorders like psoriasis. We established that the RNA substrate is cooperatively recognized by the PIN and ZnF domains of ZC3H12C and analyzed the crystal structure of ZC3H12C bound to a single-stranded RNA substrate. The RNA engages in hydrogen-bonded contacts and stacking interactions with the PIN and ZnF domains simultaneously. The ZC3H12 ZnF shows unprecedented structural features not previously observed in any member of the CCCH-ZnF family and utilizes stacking interactions via a unique combination of spatially conserved aromatic residues to align the target transcript in a bent conformation onto the ZnF scaffold. Further comparative structural analysis of ZC3H12 CCCH-ZnF suggests that a trinucleotide sequence is recognized by ZC3H12 ZnF in target RNA. Our work not only describes the initial structure-biochemical study on ZC3H12C, but also provides the first molecular insight into RNA recognition by a ZC3H12 family member. Finally, our work points to an evolutionary code for RNA recognition adopted by CCCH-type ZnF proteins.

  • Organizational Affiliation

    Macromolecular Structure and Interaction, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ribonuclease ZC3H12C
A, B
192Mus musculusMutation(s): 0 
Gene Names: Zc3h12cKiaa1726
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5DTV4 (Mus musculus)
Explore Q5DTV4 
Go to UniProtKB:  Q5DTV4
IMPC:  MGI:3026959
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5DTV4
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*UP*AP*UP*UP*AP*U)-3')7synthetic construct
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
M [auth B]ZINC ION
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
H [auth B]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
C2 H6 O2
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
N [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.248α = 90
b = 63.248β = 90
c = 114.544γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata scaling
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2021-05-26
    Changes: Derived calculations
  • Version 1.2: 2021-06-02
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Database references, Refinement description