7A8P

Structure of human mitochondrial RNA polymerase in complex with IMT inhibitor.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Small-molecule inhibitors of human mitochondrial DNA transcription.

Bonekamp, N.A.Peter, B.Hillen, H.S.Felser, A.Bergbrede, T.Choidas, A.Horn, M.Unger, A.Di Lucrezia, R.Atanassov, I.Li, X.Koch, U.Menninger, S.Boros, J.Habenberger, P.Giavalisco, P.Cramer, P.Denzel, M.S.Nussbaumer, P.Klebl, B.Falkenberg, M.Gustafsson, C.M.Larsson, N.G.

(2020) Nature 588: 712-716

  • DOI: 10.1038/s41586-020-03048-z
  • Primary Citation of Related Structures:  
    7A8P

  • PubMed Abstract: 
  • Altered expression of mitochondrial DNA (mtDNA) occurs in ageing and a range of human pathologies (for example, inborn errors of metabolism, neurodegeneration and cancer). Here we describe first-in-class specific inhibitors of mitochondrial transcription (IMTs) that target the human mitochondrial RNA polymerase (POLRMT), which is essential for biogenesis of the oxidative phosphorylation (OXPHOS) system 1-6 ...

    Altered expression of mitochondrial DNA (mtDNA) occurs in ageing and a range of human pathologies (for example, inborn errors of metabolism, neurodegeneration and cancer). Here we describe first-in-class specific inhibitors of mitochondrial transcription (IMTs) that target the human mitochondrial RNA polymerase (POLRMT), which is essential for biogenesis of the oxidative phosphorylation (OXPHOS) system 1-6 . The IMTs efficiently impair mtDNA transcription in a reconstituted recombinant system and cause a dose-dependent inhibition of mtDNA expression and OXPHOS in cell lines. To verify the cellular target, we performed exome sequencing of mutagenized cells and identified a cluster of amino acid substitutions in POLRMT that cause resistance to IMTs. We obtained a cryo-electron microscopy (cryo-EM) structure of POLRMT bound to an IMT, which further defined the allosteric binding site near the active centre cleft of POLRMT. The growth of cancer cells and the persistence of therapy-resistant cancer stem cells has previously been reported to depend on OXPHOS 7-17 , and we therefore investigated whether IMTs have anti-tumour effects. Four weeks of oral treatment with an IMT is well-tolerated in mice and does not cause OXPHOS dysfunction or toxicity in normal tissues, despite inducing a strong anti-tumour response in xenografts of human cancer cells. In summary, IMTs provide a potent and specific chemical biology tool to study the role of mtDNA expression in physiology and disease.


    Organizational Affiliation

    Max Planck Institute for Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden. nils-goran.larsson@ki.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase, mitochondrialA1143Homo sapiensMutation(s): 1 
Gene Names: POLRMT
EC: 2.7.7.6
UniProt & NIH Common Fund Data Resources
Find proteins for O00411 (Homo sapiens)
Explore O00411 
Go to UniProtKB:  O00411
PHAROS:  O00411
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R4Q
Query on R4Q

Download Ideal Coordinates CCD File 
B [auth A](3~{R})-1-[(2~{R})-2-[4-(2-chloranyl-4-fluoranyl-phenyl)-2-oxidanylidene-chromen-7-yl]oxypropanoyl]piperidine-3-carboxylic acid
C24 H21 Cl F N O6
PFEKWBKJUBCXDT-ZIAGYGMSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2015-00418
Swedish Research CouncilSweden2013-3621
Swedish Research CouncilSweden2012-2583
Knut and Alice Wallenberg FoundationSweden--
German Research Foundation (DFG)GermanySFB1218/A06
European Research Council (ERC)SwedenAdvanced Grant 2016-741366
Swedish Research CouncilSwedenALFGBG-727491
Swedish Research CouncilSwedenALFGBG-728151
Swedish Research CouncilSwedenSLL2018.0471
German Research Foundation (DFG)GermanySFB860
German Research Foundation (DFG)GermanySPP1935
European Research Council (ERC)Germany693023
Volkswagen FoundationGermany--
German Research Foundation (DFG)GermanyEXC 2067/1- 390729940
German Research Foundation (DFG)GermanyFOR2848

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-01-06
    Changes: Database references