4IKP | pdb_00004ikp

Crystal structure of coactivator-associated arginine methyltransferase 1 with methylenesinefungin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.231 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4IKP

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

A chemical probe of CARM1 alters epigenetic plasticity against breast cancer cell invasion.

Cai, X.C.Zhang, T.Kim, E.J.Jiang, M.Wang, K.Wang, J.Chen, S.Zhang, N.Wu, H.Li, F.Dela Sena, C.C.Zeng, H.Vivcharuk, V.Niu, X.Zheng, W.Lee, J.P.Chen, Y.Barsyte, D.Szewczyk, M.Hajian, T.Ibanez, G.Dong, A.Dombrovski, L.Zhang, Z.Deng, H.Min, J.Arrowsmith, C.H.Mazutis, L.Shi, L.Vedadi, M.Brown, P.J.Xiang, J.Qin, L.X.Xu, W.Luo, M.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.47110
  • Primary Citation Related Structures: 
    4IKP, 6D2L

  • PubMed Abstract: 

    CARM1 is a cancer-relevant protein arginine methyltransferase that regulates many aspects of transcription. Its pharmacological inhibition is a promising anti-cancer strategy. Here SKI-73 ( 6a in this work) is presented as a CARM1 chemical probe with pro-drug properties. SKI-73 ( 6a ) can rapidly penetrate cell membranes and then be processed into active inhibitors, which are retained intracellularly with 10-fold enrichment for several days. These compounds were characterized for their potency, selectivity, modes of action , and on-target engagement. SKI-73 ( 6a ) recapitulates the effect of CARM1 knockout against breast cancer cell invasion. Single-cell RNA-seq analysis revealed that the SKI-73 ( 6a )-associated reduction of invasiveness acts by altering epigenetic plasticity and suppressing the invasion-prone subpopulation. Interestingly, SKI-73 ( 6a ) and CARM1 knockout alter the epigenetic plasticity with remarkable difference, suggesting distinct modes of action for small-molecule and genetic perturbations. We therefore discovered a CARM1-addiction mechanism of cancer metastasis and developed a chemical probe to target this process.


  • Organizational Affiliation
    • Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.

Macromolecule Content 

  • Total Structure Weight: 157.03 kDa 
  • Atom Count: 11,705 
  • Modeled Residue Count: 1,336 
  • Deposited Residue Count: 1,364 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone-arginine methyltransferase CARM1
A, B, C, D
341Homo sapiensMutation(s): 0 
Gene Names: CARM1PRMT4
EC: 2.1.1 (PDB Primary Data), 2.1.1.125 (PDB Primary Data), 2.1.1.319 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q86X55 (Homo sapiens)
Explore Q86X55 
Go to UniProtKB:  Q86X55
PHAROS:  Q86X55
GTEx:  ENSG00000142453 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86X55
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4IK

Query on 4IK



Download:Ideal Coordinates CCD File
E [auth A],
GA [auth C],
Q [auth B],
TA [auth D]
(2S,5S)-2,6-diamino-5-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}hexanoic acid
C16 H25 N7 O5
CPUNUFGYWFHFOF-TVDBPQCTSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A],
HA [auth C],
IA [auth C],
JA [auth C],
UA [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
UNX

Query on UNX



Download:Ideal Coordinates CCD File
AA [auth B]
AB [auth D]
BA [auth B]
CA [auth B]
DA [auth B]
AA [auth B],
AB [auth D],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
M [auth A],
MA [auth C],
N [auth A],
NA [auth C],
O [auth A],
OA [auth C],
P [auth A],
PA [auth C],
QA [auth C],
R [auth B],
RA [auth C],
S [auth B],
SA [auth C],
T [auth B],
U [auth B],
V [auth B],
VA [auth D],
W [auth B],
WA [auth D],
X [auth B],
XA [auth D],
Y [auth B],
YA [auth D],
Z [auth B],
ZA [auth D]
UNKNOWN ATOM OR ION
X

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.231 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.06α = 90
b = 98.844β = 90
c = 206.628γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-05-15
    Changes: Structure summary
  • Version 1.2: 2018-01-24
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2018-04-18
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2023-09-20
    Changes: Refinement description