6IS0 | pdb_00006is0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.214 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history

Literature

Cap-specific terminal N 6 -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: https://doi.org/10.1126/science.aav0080
  • Primary Citation Related Structures: 
    6IRV, 6IRW, 6IRX, 6IRY, 6IRZ, 6IS0

  • PubMed Abstract: 

    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
    • Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.

Macromolecule Content 

  • Total Structure Weight: 60.03 kDa 
  • Atom Count: 4,286 
  • Modeled Residue Count: 470 
  • Deposited Residue Count: 499 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PDX1 C-terminal-inhibiting factor 1496Danio rerioMutation(s): 2 
Gene Names: pcif1
EC: 2.1.1.62
UniProt
Find proteins for A0A0R4IKJ1 (Danio rerio)
Explore A0A0R4IKJ1 
Go to UniProtKB:  A0A0R4IKJ1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0R4IKJ1
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
m7G-capped RNAB [auth C]3synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M7G

Query on M7G



Download:Ideal Coordinates CCD File
D [auth A]7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
C11 H18 N5 O11 P2
SBASPRRECYVBRF-KQYNXXCUSA-O
SAH

Query on SAH



Download:Ideal Coordinates CCD File
C [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
B3P

Query on B3P



Download:Ideal Coordinates CCD File
I [auth A]2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.214 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.219α = 90
b = 84.035β = 90
c = 92.97γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references
  • Version 1.2: 2020-10-28
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2024-03-06
    Changes: Data collection, Non-polymer description, Structure summary