6V0N

PRMT5 bound to PBM peptide from Riok1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Molecular basis for substrate recruitment to the PRMT5 methylosome.

Mulvaney, K.M., Blomquist, C., Acharya, N., Li, R., Ranaghan, M.J., O'Keefe, M., Rodriguez, D.J., Young, M.J., Kesar, D., Pal, D., Stokes, M., Nelson, A.J., Jain, S.S., Yang, A., Mullin-Bernstein, Z., Columbus, J., Bozal, F.K., Skepner, A., Raymond, D., LaRussa, S., McKinney, D.C., Freyzon, Y., Baidi, Y., Porter, D., Aguirre, A.J., Ianari, A., McMillan, B., Sellers, W.R.

(2021) Mol Cell 81: 3481

  • DOI: https://doi.org/10.1016/j.molcel.2021.07.019
  • Primary Citation of Related Structures:  
    6V0N, 6V0O

  • PubMed Abstract: 

    • PRMT5 is an essential arginine methyltransferase and a therapeutic target in MTAP-null cancers. PRMT5 uses adaptor proteins for substrate recruitment through a previously undefined mechanism. Here, we identify an evolutionarily conserved peptide sequence shared among the three known substrate adaptors (CLNS1A, RIOK1, and COPR5) and show that it is necessary and sufficient for interaction with PRMT5 ...

    PRMT5 is an essential arginine methyltransferase and a therapeutic target in MTAP-null cancers. PRMT5 uses adaptor proteins for substrate recruitment through a previously undefined mechanism. Here, we identify an evolutionarily conserved peptide sequence shared among the three known substrate adaptors (CLNS1A, RIOK1, and COPR5) and show that it is necessary and sufficient for interaction with PRMT5. We demonstrate that PRMT5 uses modular adaptor proteins containing a common binding motif for substrate recruitment, comparable with other enzyme classes such as kinases and E3 ligases. We structurally resolve the interface with PRMT5 and show via genetic perturbation that it is required for methylation of adaptor-recruited substrates including the spliceosome, histones, and ribosomal complexes. Furthermore, disruption of this site affects Sm spliceosome activity, leading to intron retention. Genetic disruption of the PRMT5-substrate adaptor interface impairs growth of MTAP-null tumor cells and is thus a site for development of therapeutic inhibitors of PRMT5.

    Organizational Affiliation: 

    Broad Institute, Cambridge, MA, USA; Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA. Electronic address: wsellers@broadinstitute.org.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 5637Homo sapiensMutation(s): 0 
Gene Names: PRMT5, HRMT1L5, IBP72, JBP1, SKB1
EC: 2.1.1.320
UniProt & NIH Common Fund Data Resources
Find proteins for O14744 (Homo sapiens)
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PHAROS:  O14744
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UniProt GroupO14744
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Methylosome protein 50342Homo sapiensMutation(s): 0 
Gene Names: WDR77, MEP50, WD45, HKMT1069, Nbla10071
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Find proteins for Q9BQA1 (Homo sapiens)
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PHAROS:  Q9BQA1
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UniProt GroupQ9BQA1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Riok1 PBM peptide13Homo sapiensMutation(s): 0 
Gene Names: RIOK1, RIO1
EC: 2.7.11.1 (UniProt), 3.6.3 (UniProt)
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Find proteins for Q9BRS2 (Homo sapiens)
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Go to UniProtKB:  Q9BRS2
PHAROS:  Q9BRS2
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UniProt GroupQ9BRS2
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SFG
Query on SFG
Download Ideal Coordinates CCD File 
D [auth A]SINEFUNGIN
C15 H23 N7 O5
LMXOHSDXUQEUSF-YECHIGJVSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.96α = 90
b = 139.41β = 90
c = 179.95γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references
  • Version 1.2: 2021-08-25
    Changes: Database references
  • Version 1.3: 2021-09-15
    Changes: Database references