6IS0

Crystal structure of the zebrafish cap-specific adenosine methyltransferase bound to SAH and m7G-capped RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cap-specific terminalN6-methylation of RNA by an RNA polymerase II-associated methyltransferase.

Akichika, S.Hirano, S.Shichino, Y.Suzuki, T.Nishimasu, H.Ishitani, R.Sugita, A.Hirose, Y.Iwasaki, S.Nureki, O.Suzuki, T.

(2019) Science 363: --

  • DOI: 10.1126/science.aav0080
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • <i>N </i> <sup>6 </sup>-methyladenosine (m <sup>6 </sup>A), a major modification of messenger RNAs (mRNAs), plays critical roles in RNA metabolism and function. In addition to the internal m <sup>6 </sup>A, <i>N </i> <sup>6 </sup>, 2'- <i>O </i>-di ...

    N 6 -methyladenosine (m 6 A), a major modification of messenger RNAs (mRNAs), plays critical roles in RNA metabolism and function. In addition to the internal m 6 A, N 6 , 2'- O -dimethyladenosine (m 6 Am) is present at the transcription start nucleotide of capped mRNAs in vertebrates. However, its biogenesis and functional role remain elusive. Using a reverse genetics approach, we identified PCIF1, a factor that interacts with the serine-5-phosphorylated carboxyl-terminal domain of RNA polymerase II, as a cap-specific adenosine methyltransferase (CAPAM) responsible for N 6 -methylation of m 6 Am. The crystal structure of CAPAM in complex with substrates revealed the molecular basis of cap-specific m 6 A formation. A transcriptome-wide analysis revealed that N 6 -methylation of m 6 Am promotes the translation of capped mRNAs. Thus, a cap-specific m 6 A writer promotes translation of mRNAs starting from m 6 Am.


    Organizational Affiliation

    RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. ts@chembio.t.u-tokyo.ac.jp nureki@bs.s.u-tokyo.ac.jp.,Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan. ts@chembio.t.u-tokyo.ac.jp nureki@bs.s.u-tokyo.ac.jp.,Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo 277-8562, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PDX1 C-terminal-inhibiting factor 1
A
496Danio rerioMutation(s): 2 
Gene Names: pcif1
EC: 2.1.1.62
Find proteins for A0A0R4IKJ1 (Danio rerio)
Go to UniProtKB:  A0A0R4IKJ1
Entity ID: 2
MoleculeChainsLengthOrganism
m7G-capped RNAC3synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B3P
Query on B3P

Download SDF File 
Download CCD File 
A
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
M7G
Query on M7G

Download SDF File 
Download CCD File 
A
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
C11 H19 N5 O11 P2
QQODJOAVWUWVHJ-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
A2M
Query on A2M
C
RNA LINKINGC11 H16 N5 O7 PA
M7G
Query on M7G
C
NON-POLYMERC11 H19 N5 O11 P2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.219α = 90.00
b = 84.035β = 90.00
c = 92.970γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2019-01-23
    Type: Data collection, Database references