6H2V

Crystal structure of human METTL5-TRMT112 complex, the 18S rRNA m6A1832 methyltransferase at 2.5A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

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Ligand Structure Quality Assessment 


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Literature

The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112.

van Tran, N.Ernst, F.G.M.Hawley, B.R.Zorbas, C.Ulryck, N.Hackert, P.Bohnsack, K.E.Bohnsack, M.T.Jaffrey, S.R.Graille, M.Lafontaine, D.L.J.

(2019) Nucleic Acids Res 47: 7719-7733

  • DOI: 10.1093/nar/gkz619
  • Primary Citation of Related Structures:  
    6H2U, 6H2V

  • PubMed Abstract: 
  • N6-methyladenosine (m6A) has recently been found abundantly on messenger RNA and shown to regulate most steps of mRNA metabolism. Several important m6A methyltransferases have been described functionally and structurally, but the enzymes responsible for installing one m6A residue on each subunit of human ribosomes at functionally important sites have eluded identification for over 30 years ...

    N6-methyladenosine (m6A) has recently been found abundantly on messenger RNA and shown to regulate most steps of mRNA metabolism. Several important m6A methyltransferases have been described functionally and structurally, but the enzymes responsible for installing one m6A residue on each subunit of human ribosomes at functionally important sites have eluded identification for over 30 years. Here, we identify METTL5 as the enzyme responsible for 18S rRNA m6A modification and confirm ZCCHC4 as the 28S rRNA modification enzyme. We show that METTL5 must form a heterodimeric complex with TRMT112, a known methyltransferase activator, to gain metabolic stability in cells. We provide the first atomic resolution structure of METTL5-TRMT112, supporting that its RNA-binding mode differs distinctly from that of other m6A RNA methyltransferases. On the basis of similarities with a DNA methyltransferase, we propose that METTL5-TRMT112 acts by extruding the adenosine to be modified from a double-stranded nucleic acid.


    Organizational Affiliation

    RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Fonds de la Recherche Scientifique (F.R.S./FNRS), Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methyltransferase-like protein 5A, C215Homo sapiensMutation(s): 0 
Gene Names: METTL5DC3HSPC133
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRN9 (Homo sapiens)
Explore Q9NRN9 
Go to UniProtKB:  Q9NRN9
PHAROS:  Q9NRN9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NRN9
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Multifunctional methyltransferase subunit TRM112-like proteinB, D125Homo sapiensMutation(s): 0 
Gene Names: TRMT112AD-001HSPC152HSPC170
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UI30 (Homo sapiens)
Explore Q9UI30 
Go to UniProtKB:  Q9UI30
PHAROS:  Q9UI30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UI30
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
E [auth A],
L [auth C]
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
PG0
Query on PG0

Download Ideal Coordinates CCD File 
M [auth C],
Q [auth D]
2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
K [auth B],
N [auth C],
F [auth A],
G [auth A],
H [auth A],
K [auth B],
N [auth C],
O [auth C],
R [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth B],
P [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
B, D L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.38α = 90
b = 105.894β = 90
c = 169.239γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-14-CE09-0016
French National Research AgencyFranceANR-16-CE11-0003

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references