Crystal structure of human ZCCHC4 in complex with SAH

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structure and regulation of ZCCHC4 in m6A-methylation of 28S rRNA.

Ren, W.Lu, J.Huang, M.Gao, L.Li, D.Wang, G.G.Song, J.

(2019) Nat Commun 10: 5042-5042

  • DOI: https://doi.org/10.1038/s41467-019-12923-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    N 6 -methyladenosine (m 6 A) modification provides an important epitranscriptomic mechanism that critically regulates RNA metabolism and function. However, how m 6 A writers attain substrate specificities remains unclear. We report the 3.1 Å-resolution crystal structure of human CCHC zinc finger-containing protein ZCCHC4, a 28S rRNA-specific m 6 A methyltransferase, bound to S-adenosyl-L-homocysteine. The methyltransferase (MTase) domain of ZCCHC4 is packed against N-terminal GRF-type and C2H2 zinc finger domains and a C-terminal CCHC domain, creating an integrated RNA-binding surface. Strikingly, the MTase domain adopts an autoinhibitory conformation, with a self-occluded catalytic site and a fully-closed cofactor pocket. Mutational and enzymatic analyses further substantiate the molecular basis for ZCCHC4-RNA recognition and a role of the stem-loop structure within substrate in governing the substrate specificity. Overall, this study unveils unique structural and enzymatic characteristics of ZCCHC4, distinctive from what was seen with the METTL family of m 6 A writers, providing the mechanistic basis for ZCCHC4 modulation of m 6 A RNA methylation.

  • Organizational Affiliation

    Department of Biochemistry, University of California, Riverside, CA, 92521, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA N6-adenosine-methyltransferase ZCCHC4
A, B, C, D, E
A, B, C, D, E, F
442Homo sapiensMutation(s): 5 
Gene Names: ZCCHC4
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H5U6 (Homo sapiens)
Explore Q9H5U6 
Go to UniProtKB:  Q9H5U6
GTEx:  ENSG00000168228 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H5U6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
BA [auth D]
G [auth A]
IA [auth E]
N [auth B]
PA [auth F]
BA [auth D],
G [auth A],
IA [auth E],
N [auth B],
PA [auth F],
U [auth C]
C14 H20 N6 O5 S
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth C]
CA [auth D]
DA [auth D]
EA [auth D]
FA [auth D]
AA [auth C],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
J [auth A],
JA [auth E],
K [auth A],
KA [auth E],
L [auth A],
LA [auth E],
M [auth A],
MA [auth E],
NA [auth E],
O [auth B],
OA [auth E],
P [auth B],
Q [auth B],
QA [auth F],
R [auth B],
RA [auth F],
S [auth B],
SA [auth F],
T [auth B],
TA [auth F],
UA [auth F],
V [auth C],
VA [auth F],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.567α = 90
b = 290.38β = 90
c = 83.529γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2020-04-29
    Changes: Database references
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references