9OHL | pdb_00009ohl

TRMT112-METTL5 bound to SAM and FWG-33B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 
    0.217 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.186 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Complexoform-restricted covalent TRMT112 ligands that allosterically agonize METTL5.

Goetzke, F.W.Bernard, S.M.Ju, C.W.Pollock, J.DeMeester, K.E.Gross, J.Simon, G.M.He, C.Melillo, B.Cravatt, B.F.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.05.25.655995
  • Primary Citation of Related Structures:  
    9OHL

  • PubMed Abstract: 

    Adaptors serve as hubs to regulate diverse protein complexes in cells. This multitude of functions can complicate the study of adaptors, as their genetic disruption may simultaneously impair the activities of several compositionally distinct complexes (or adaptor 'complexoforms'). Here we describe the chemical proteomic discovery of bicyclopyrrolidine acrylamide stereoprobes that react with cysteine-100 (C100) of the methyltransferase (MT) adaptor TRMT112 in human cells. Curiously, the stereoprobes showed negligible reactivity with uncomplexed recombinant TRMT112, and we found that this interaction was restored excluively in the presence of METTL5, but not other MTs. A co-crystal structure revealed stereoprobe binding to a composite pocket proximal to C100 of TRMT112 that is templated by METTL5 and absent in other TRMT112:MT complexes. Structural rearrangements promoted by stereoprobe binding in turn lead to allosteric agonism of METTL5, thus revealing how covalent ligands targeting a pleiotropic adaptor can confer partner-specific functional effects through reactivity with a single complexoform.


  • Organizational Affiliation
    • Department of Chemistry, Scripps Research, La Jolla, CA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA N(6)-adenosine-methyltransferase METTL5A [auth C]209Homo 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
GTEx:  ENSG00000138382 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NRN9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Multifunctional methyltransferase subunit TRM112-like proteinB [auth D]125Homo 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
GTEx:  ENSG00000173113 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UI30
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CBE (Subject of Investigation/LOI)
Query on A1CBE

Download Ideal Coordinates CCD File 
D
N-(4-{[(3aS,4R,6S,6aR)-6-(3-chlorophenyl)-2-propanoyloctahydrocyclopenta[c]pyrrol-4-yl]oxy}phenyl)acetamide
C24 H27 Cl N2 O3
BEXJJYBHLWEKDU-SSGKUCQKSA-N
SAM
Query on SAM

Download Ideal Coordinates CCD File 
C
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free:  0.217 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.684α = 90
b = 70.64β = 90
c = 84.553γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR35 CA231991
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-06-18
    Changes: Database references