5FA5

Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Disordered methionine metabolism in MTAP/CDKN2A-deleted cancers leads to dependence on PRMT5.

Mavrakis, K.J., McDonald, E.R., Schlabach, M.R., Billy, E., Hoffman, G.R., deWeck, A., Ruddy, D.A., Venkatesan, K., Yu, J., McAllister, G., Stump, M., deBeaumont, R., Ho, S., Yue, Y., Liu, Y., Yan-Neale, Y., Yang, G., Lin, F., Yin, H., Gao, H., Kipp, D.R., Zhao, S., McNamara, J.T., Sprague, E.R., Zheng, B., Lin, Y., Cho, Y.S., Gu, J., Crawford, K., Ciccone, D., Vitari, A.C., Lai, A., Capka, V., Hurov, K., Porter, J.A., Tallarico, J., Mickanin, C., Lees, E., Pagliarini, R., Keen, N., Schmelzle, T., Hofmann, F., Stegmeier, F., Sellers, W.R.

(2016) Science 351: 1208-1213

  • DOI: 10.1126/science.aad5944
  • Primary Citation of Related Structures:  
    5FA5

  • PubMed Abstract: 

    • 5-Methylthioadenosine phosphorylase (MTAP) is a key enzyme in the methionine salvage pathway. The MTAP gene is frequently deleted in human cancers because of its chromosomal proximity to the tumor suppressor gene CDKN2A. By interrogating data from a ...

    5-Methylthioadenosine phosphorylase (MTAP) is a key enzyme in the methionine salvage pathway. The MTAP gene is frequently deleted in human cancers because of its chromosomal proximity to the tumor suppressor gene CDKN2A. By interrogating data from a large-scale short hairpin RNA-mediated screen across 390 cancer cell line models, we found that the viability of MTAP-deficient cancer cells is impaired by depletion of the protein arginine methyltransferase PRMT5. MTAP-deleted cells accumulate the metabolite methylthioadenosine (MTA), which we found to inhibit PRMT5 methyltransferase activity. Deletion of MTAP in MTAP-proficient cells rendered them sensitive to PRMT5 depletion. Conversely, reconstitution of MTAP in an MTAP-deficient cell line rescued PRMT5 dependence. Thus, MTA accumulation in MTAP-deleted cancers creates a hypomorphic PRMT5 state that is selectively sensitized toward further PRMT5 inhibition. Inhibitors of PRMT5 that leverage this dysregulated metabolic state merit further investigation as a potential therapy for MTAP/CDKN2A-deleted tumors.

    Organizational Affiliation: 

    Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA. william.sellers@novartis.com fstegmeier@ksqtx.com.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 5A650Homo sapiensMutation(s): 0 
Gene Names: PRMT5, HRMT1L5, IBP72, JBP1, SKB1
EC: 2.1.1 (PDB Primary Data), 2.1.1.125 (PDB Primary Data), 2.1.1.320 (UniProt)
Find proteins for O14744 (Homo sapiens)
Explore O14744 
Go to UniProtKB:  O14744
NIH Common Fund Data Resources
PHAROS  O14744
GTEx  ENSG00000100462
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Methylosome protein 50B367Homo sapiensMutation(s): 0 
Gene Names: WDR77, MEP50, WD45, HKMT1069, Nbla10071
Find proteins for Q9BQA1 (Homo sapiens)
Explore Q9BQA1 
Go to UniProtKB:  Q9BQA1
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PHAROS  Q9BQA1
GTEx  ENSG00000116455
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4C20Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805
GTEx  ENSG00000274618GTEx  ENSG00000197238GTEx  ENSG00000197837GTEx  ENSG00000158406GTEx  ENSG00000278705GTEx  ENSG00000197061GTEx  ENSG00000270882GTEx  ENSG00000270276GTEx  ENSG00000273542GTEx  ENSG00000277157GTEx  ENSG00000276966GTEx  ENSG00000276180GTEx  ENSG00000278637GTEx  ENSG00000275126
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTA
Query on MTA
Download Ideal Coordinates CCD File 
A
5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MTAIC50:  4600   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.05α = 90
b = 137.85β = 90
c = 178.43γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 1.2: 2016-03-23
    Changes: Database references