6UCA

Crystal structure of human ZCCHC4 in complex with SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.281 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.249 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.250 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SAHClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

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:  
    6UCA

  • 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.


Macromolecules
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
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
PHAROS:  Q9H5U6
GTEx:  ENSG00000168228 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H5U6
Sequence Annotations
Expand
  • 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]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
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]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.281 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.249 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.250 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.567α = 90
b = 290.38β = 90
c = 83.529γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
CRANK2phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SAHClick on this verticalbar to view details

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